Starting phenix.real_space_refine on Wed Apr 8 01:56:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r1g_18810/04_2026/8r1g_18810.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r1g_18810/04_2026/8r1g_18810.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8r1g_18810/04_2026/8r1g_18810.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r1g_18810/04_2026/8r1g_18810.map" model { file = "/net/cci-nas-00/data/ceres_data/8r1g_18810/04_2026/8r1g_18810.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r1g_18810/04_2026/8r1g_18810.cif" } resolution = 3.99 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= -0.001 sd= 0.092 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 6 6.06 5 S 112 5.16 5 C 10610 2.51 5 N 2862 2.21 5 O 3142 1.98 5 H 16526 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33258 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 11110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 681, 11110 Classifications: {'peptide': 681} Link IDs: {'PTRANS': 28, 'TRANS': 652} Chain breaks: 1 Chain: "B" Number of atoms: 2365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 2365 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "C" Number of atoms: 3151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 3151 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 15, 'TRANS': 186} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12835 SG CYS B 110 73.866 102.944 46.248 1.00 88.62 S ATOM 12878 SG CYS B 113 74.283 103.712 42.874 1.00 87.95 S ATOM 13405 SG CYS B 143 76.342 100.773 44.385 1.00 87.19 S ATOM 13429 SG CYS B 146 77.307 104.282 45.198 1.00 93.27 S ATOM 11605 SG CYS B 37 66.178 114.896 36.868 1.00114.45 S ATOM 11652 SG CYS B 40 67.616 118.161 36.171 1.00108.22 S ATOM 12158 SG CYS B 70 69.841 114.908 36.696 1.00103.60 S ATOM 12202 SG CYS B 73 68.199 116.574 39.588 1.00 99.17 S ATOM 14814 SG CYS C 176 65.958 71.313 19.330 1.00187.28 S ATOM 15777 SG CYS C 238 64.381 73.597 22.216 1.00182.95 S ATOM 15823 SG CYS C 242 68.011 73.982 21.267 1.00171.60 S Restraints were copied for chains: D, E, F Time building chain proxies: 16.14, per 1000 atoms: 0.49 Number of scatterers: 33258 At special positions: 0 Unit cell: (159.6, 152.88, 122.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 6 29.99 S 112 16.00 O 3142 8.00 N 2862 7.00 C 10610 6.00 H 16526 1.00 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: 3.28 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 201 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 110 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 143 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 146 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 113 " pdb=" ZN B 202 " pdb="ZN ZN B 202 " - pdb=" SG CYS B 37 " pdb="ZN ZN B 202 " - pdb=" SG CYS B 40 " pdb="ZN ZN B 202 " - pdb=" SG CYS B 73 " pdb="ZN ZN B 202 " - pdb=" SG CYS B 70 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" ND1 HIS C 179 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 238 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 176 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 242 " pdb=" ZN E 201 " pdb="ZN ZN E 201 " - pdb=" SG CYS E 110 " pdb="ZN ZN E 201 " - pdb=" SG CYS E 113 " pdb="ZN ZN E 201 " - pdb=" SG CYS E 143 " pdb="ZN ZN E 201 " - pdb=" SG CYS E 146 " pdb=" ZN E 202 " pdb="ZN ZN E 202 " - pdb=" SG CYS E 37 " pdb="ZN ZN E 202 " - pdb=" SG CYS E 40 " pdb="ZN ZN E 202 " - pdb=" SG CYS E 73 " pdb="ZN ZN E 202 " - pdb=" SG CYS E 70 " pdb=" ZN F 401 " pdb="ZN ZN F 401 " - pdb=" ND1 HIS F 179 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 238 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 176 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 242 " Number of angles added : 30 4068 Ramachandran restraints generated. 2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3904 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 18 sheets defined 56.4% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 129 through 143 removed outlier: 3.853A pdb=" N ILE A 136 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 139 " --> pdb=" O GLU A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 158 Processing helix chain 'A' and resid 159 through 167 removed outlier: 4.168A pdb=" N PHE A 167 " --> pdb=" O LEU A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 247 Processing helix chain 'A' and resid 249 through 274 removed outlier: 3.507A pdb=" N ALA A 255 " --> pdb=" O LYS A 251 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR A 262 " --> pdb=" O ASN A 258 " (cutoff:3.500A) Proline residue: A 265 - end of helix removed outlier: 3.513A pdb=" N CYS A 269 " --> pdb=" O PRO A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 280 removed outlier: 3.570A pdb=" N ARG A 279 " --> pdb=" O ASN A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 283 No H-bonds generated for 'chain 'A' and resid 281 through 283' Processing helix chain 'A' and resid 284 through 292 Processing helix chain 'A' and resid 293 through 297 removed outlier: 3.668A pdb=" N LEU A 296 " --> pdb=" O ASN A 293 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N HIS A 297 " --> pdb=" O ARG A 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 293 through 297' Processing helix chain 'A' and resid 298 through 304 removed outlier: 4.278A pdb=" N MET A 304 " --> pdb=" O GLU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 314 Processing helix chain 'A' and resid 317 through 329 Processing helix chain 'A' and resid 332 through 354 removed outlier: 3.538A pdb=" N LEU A 346 " --> pdb=" O THR A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 364 Processing helix chain 'A' and resid 365 through 386 Processing helix chain 'A' and resid 403 through 413 Processing helix chain 'A' and resid 426 through 433 Processing helix chain 'A' and resid 435 through 437 No H-bonds generated for 'chain 'A' and resid 435 through 437' Processing helix chain 'A' and resid 445 through 450 Processing helix chain 'A' and resid 451 through 458 Processing helix chain 'A' and resid 459 through 469 Processing helix chain 'A' and resid 476 through 484 Proline residue: A 481 - end of helix Processing helix chain 'A' and resid 485 through 516 Processing helix chain 'A' and resid 531 through 547 Processing helix chain 'A' and resid 549 through 553 Processing helix chain 'A' and resid 568 through 584 Processing helix chain 'A' and resid 585 through 588 Processing helix chain 'A' and resid 608 through 625 removed outlier: 3.990A pdb=" N PHE A 612 " --> pdb=" O THR A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 642 removed outlier: 4.081A pdb=" N TYR A 638 " --> pdb=" O PRO A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 649 No H-bonds generated for 'chain 'A' and resid 647 through 649' Processing helix chain 'A' and resid 650 through 655 removed outlier: 3.825A pdb=" N SER A 654 " --> pdb=" O ASP A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 668 removed outlier: 3.572A pdb=" N SER A 661 " --> pdb=" O VAL A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 677 Processing helix chain 'A' and resid 699 through 703 Processing helix chain 'A' and resid 709 through 723 Processing helix chain 'A' and resid 726 through 742 removed outlier: 3.711A pdb=" N ALA A 732 " --> pdb=" O LYS A 728 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VAL A 740 " --> pdb=" O GLY A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 750 Processing helix chain 'A' and resid 751 through 761 removed outlier: 3.662A pdb=" N LEU A 757 " --> pdb=" O GLU A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 774 Processing helix chain 'A' and resid 784 through 797 Processing helix chain 'A' and resid 798 through 811 Processing helix chain 'A' and resid 819 through 823 Processing helix chain 'A' and resid 854 through 869 Processing helix chain 'B' and resid 18 through 26 Processing helix chain 'B' and resid 45 through 55 Processing helix chain 'B' and resid 70 through 85 Processing helix chain 'B' and resid 92 through 100 Processing helix chain 'B' and resid 102 through 106 Processing helix chain 'B' and resid 118 through 128 Processing helix chain 'B' and resid 143 through 148 Processing helix chain 'C' and resid 104 through 108 removed outlier: 3.866A pdb=" N TYR C 107 " --> pdb=" O GLN C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 169 Processing helix chain 'C' and resid 176 through 181 Processing helix chain 'C' and resid 277 through 292 Processing helix chain 'D' and resid 129 through 143 removed outlier: 3.843A pdb=" N ILE D 136 " --> pdb=" O LYS D 132 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU D 139 " --> pdb=" O GLU D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 158 Processing helix chain 'D' and resid 159 through 167 removed outlier: 4.170A pdb=" N PHE D 167 " --> pdb=" O LEU D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 247 Processing helix chain 'D' and resid 249 through 274 removed outlier: 3.510A pdb=" N ALA D 255 " --> pdb=" O LYS D 251 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR D 262 " --> pdb=" O ASN D 258 " (cutoff:3.500A) Proline residue: D 265 - end of helix removed outlier: 3.518A pdb=" N CYS D 269 " --> pdb=" O PRO D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 280 removed outlier: 3.566A pdb=" N ARG D 279 " --> pdb=" O ASN D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 283 No H-bonds generated for 'chain 'D' and resid 281 through 283' Processing helix chain 'D' and resid 284 through 292 Processing helix chain 'D' and resid 293 through 297 removed outlier: 3.658A pdb=" N LEU D 296 " --> pdb=" O ASN D 293 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N HIS D 297 " --> pdb=" O ARG D 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 293 through 297' Processing helix chain 'D' and resid 298 through 304 removed outlier: 4.285A pdb=" N MET D 304 " --> pdb=" O GLU D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 314 Processing helix chain 'D' and resid 317 through 329 Processing helix chain 'D' and resid 332 through 354 removed outlier: 3.538A pdb=" N LEU D 346 " --> pdb=" O THR D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 364 Processing helix chain 'D' and resid 365 through 386 Processing helix chain 'D' and resid 403 through 413 Processing helix chain 'D' and resid 426 through 433 Processing helix chain 'D' and resid 435 through 437 No H-bonds generated for 'chain 'D' and resid 435 through 437' Processing helix chain 'D' and resid 445 through 450 Processing helix chain 'D' and resid 451 through 458 Processing helix chain 'D' and resid 459 through 469 Processing helix chain 'D' and resid 476 through 484 Proline residue: D 481 - end of helix Processing helix chain 'D' and resid 485 through 516 Processing helix chain 'D' and resid 531 through 547 Processing helix chain 'D' and resid 549 through 553 Processing helix chain 'D' and resid 568 through 584 Processing helix chain 'D' and resid 585 through 588 Processing helix chain 'D' and resid 608 through 625 removed outlier: 3.990A pdb=" N PHE D 612 " --> pdb=" O THR D 608 " (cutoff:3.500A) Processing helix chain 'D' and resid 634 through 642 removed outlier: 4.084A pdb=" N TYR D 638 " --> pdb=" O PRO D 634 " (cutoff:3.500A) Processing helix chain 'D' and resid 647 through 649 No H-bonds generated for 'chain 'D' and resid 647 through 649' Processing helix chain 'D' and resid 650 through 655 removed outlier: 3.825A pdb=" N SER D 654 " --> pdb=" O ASP D 650 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 668 removed outlier: 3.572A pdb=" N SER D 661 " --> pdb=" O VAL D 657 " (cutoff:3.500A) Processing helix chain 'D' and resid 671 through 677 Processing helix chain 'D' and resid 699 through 703 Processing helix chain 'D' and resid 709 through 723 Processing helix chain 'D' and resid 726 through 742 removed outlier: 3.711A pdb=" N ALA D 732 " --> pdb=" O LYS D 728 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL D 740 " --> pdb=" O GLY D 736 " (cutoff:3.500A) Processing helix chain 'D' and resid 745 through 750 Processing helix chain 'D' and resid 751 through 761 removed outlier: 3.663A pdb=" N LEU D 757 " --> pdb=" O GLU D 753 " (cutoff:3.500A) Processing helix chain 'D' and resid 766 through 774 Processing helix chain 'D' and resid 784 through 797 Processing helix chain 'D' and resid 798 through 811 Processing helix chain 'D' and resid 819 through 823 Processing helix chain 'D' and resid 854 through 869 Processing helix chain 'E' and resid 18 through 26 Processing helix chain 'E' and resid 45 through 55 Processing helix chain 'E' and resid 70 through 85 Processing helix chain 'E' and resid 92 through 100 Processing helix chain 'E' and resid 102 through 106 Processing helix chain 'E' and resid 118 through 128 Processing helix chain 'E' and resid 143 through 148 Processing helix chain 'F' and resid 104 through 108 removed outlier: 3.867A pdb=" N TYR F 107 " --> pdb=" O GLN F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 169 Processing helix chain 'F' and resid 176 through 181 Processing helix chain 'F' and resid 277 through 292 Processing sheet with id=AA1, first strand: chain 'A' and resid 387 through 388 removed outlier: 6.544A pdb=" N GLU A 387 " --> pdb=" O ARG A 440 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 522 through 527 Processing sheet with id=AA3, first strand: chain 'A' and resid 590 through 593 removed outlier: 3.680A pdb=" N LEU A 598 " --> pdb=" O ASP A 593 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 681 through 685 Processing sheet with id=AA5, first strand: chain 'A' and resid 775 through 777 removed outlier: 6.609A pdb=" N GLU A 775 " --> pdb=" O ILE A 827 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N LYS A 829 " --> pdb=" O GLU A 775 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ASP A 777 " --> pdb=" O LYS A 829 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE A 826 " --> pdb=" O LEU A 847 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LEU A 849 " --> pdb=" O ILE A 826 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ALA A 828 " --> pdb=" O LEU A 849 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 36 through 37 removed outlier: 6.311A pdb=" N GLU B 36 " --> pdb=" O ALA B 68 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 86 through 91 removed outlier: 3.816A pdb=" N TYR B 88 " --> pdb=" O ASN B 134 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ARG B 109 " --> pdb=" O GLY B 141 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 110 through 113 removed outlier: 4.507A pdb=" N HIS C 233 " --> pdb=" O GLU C 198 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 124 through 127 removed outlier: 4.208A pdb=" N ILE C 251 " --> pdb=" O VAL C 272 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ALA C 161 " --> pdb=" O HIS C 214 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N HIS C 214 " --> pdb=" O ALA C 161 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 387 through 388 removed outlier: 6.543A pdb=" N GLU D 387 " --> pdb=" O ARG D 440 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 522 through 527 Processing sheet with id=AB3, first strand: chain 'D' and resid 590 through 593 removed outlier: 3.679A pdb=" N LEU D 598 " --> pdb=" O ASP D 593 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 681 through 685 Processing sheet with id=AB5, first strand: chain 'D' and resid 775 through 777 removed outlier: 6.608A pdb=" N GLU D 775 " --> pdb=" O ILE D 827 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N LYS D 829 " --> pdb=" O GLU D 775 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ASP D 777 " --> pdb=" O LYS D 829 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE D 826 " --> pdb=" O LEU D 847 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LEU D 849 " --> pdb=" O ILE D 826 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ALA D 828 " --> pdb=" O LEU D 849 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 36 through 37 removed outlier: 6.312A pdb=" N GLU E 36 " --> pdb=" O ALA E 68 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 86 through 91 removed outlier: 3.818A pdb=" N TYR E 88 " --> pdb=" O ASN E 134 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ARG E 109 " --> pdb=" O GLY E 141 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 110 through 113 removed outlier: 4.507A pdb=" N HIS F 233 " --> pdb=" O GLU F 198 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 124 through 127 removed outlier: 4.196A pdb=" N ILE F 251 " --> pdb=" O VAL F 272 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ALA F 161 " --> pdb=" O HIS F 214 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N HIS F 214 " --> pdb=" O ALA F 161 " (cutoff:3.500A) 844 hydrogen bonds defined for protein. 2352 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: 7.55 Time building geometry restraints manager: 4.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 16490 1.03 - 1.23: 209 1.23 - 1.43: 7003 1.43 - 1.63: 9738 1.63 - 1.82: 166 Bond restraints: 33606 Sorted by residual: bond pdb=" N VAL D 234 " pdb=" H VAL D 234 " ideal model delta sigma weight residual 0.860 0.962 -0.102 2.00e-02 2.50e+03 2.58e+01 bond pdb=" N VAL A 234 " pdb=" H VAL A 234 " ideal model delta sigma weight residual 0.860 0.961 -0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" CB ASN A 258 " pdb=" CG ASN A 258 " ideal model delta sigma weight residual 1.516 1.460 0.056 2.50e-02 1.60e+03 4.93e+00 bond pdb=" CE LYS D 311 " pdb=" NZ LYS D 311 " ideal model delta sigma weight residual 1.489 1.426 0.063 3.00e-02 1.11e+03 4.46e+00 bond pdb=" C ILE A 401 " pdb=" N PRO A 402 " ideal model delta sigma weight residual 1.330 1.354 -0.024 1.25e-02 6.40e+03 3.82e+00 ... (remaining 33601 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 57716 1.75 - 3.50: 2766 3.50 - 5.24: 175 5.24 - 6.99: 25 6.99 - 8.74: 6 Bond angle restraints: 60688 Sorted by residual: angle pdb=" CB ARG A 500 " pdb=" CG ARG A 500 " pdb=" CD ARG A 500 " ideal model delta sigma weight residual 111.30 102.62 8.68 2.30e+00 1.89e-01 1.42e+01 angle pdb=" CB ARG D 500 " pdb=" CG ARG D 500 " pdb=" CD ARG D 500 " ideal model delta sigma weight residual 111.30 102.66 8.64 2.30e+00 1.89e-01 1.41e+01 angle pdb=" C GLU A 135 " pdb=" CA GLU A 135 " pdb=" CB GLU A 135 " ideal model delta sigma weight residual 110.46 103.63 6.83 1.94e+00 2.66e-01 1.24e+01 angle pdb=" C GLU D 135 " pdb=" CA GLU D 135 " pdb=" CB GLU D 135 " ideal model delta sigma weight residual 110.46 103.64 6.82 1.94e+00 2.66e-01 1.24e+01 angle pdb=" C PHE D 256 " pdb=" CA PHE D 256 " pdb=" CB PHE D 256 " ideal model delta sigma weight residual 110.88 106.15 4.73 1.57e+00 4.06e-01 9.07e+00 ... (remaining 60683 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.92: 14271 15.92 - 31.85: 918 31.85 - 47.77: 315 47.77 - 63.70: 258 63.70 - 79.62: 70 Dihedral angle restraints: 15832 sinusoidal: 8702 harmonic: 7130 Sorted by residual: dihedral pdb=" CD ARG A 500 " pdb=" NE ARG A 500 " pdb=" CZ ARG A 500 " pdb=" NH1 ARG A 500 " ideal model delta sinusoidal sigma weight residual 0.00 36.47 -36.47 1 1.00e+01 1.00e-02 1.88e+01 dihedral pdb=" CD ARG D 500 " pdb=" NE ARG D 500 " pdb=" CZ ARG D 500 " pdb=" NH1 ARG D 500 " ideal model delta sinusoidal sigma weight residual 0.00 36.40 -36.40 1 1.00e+01 1.00e-02 1.87e+01 dihedral pdb=" CA ASN D 723 " pdb=" C ASN D 723 " pdb=" N LYS D 724 " pdb=" CA LYS D 724 " ideal model delta harmonic sigma weight residual -180.00 -160.87 -19.13 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 15829 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1591 0.053 - 0.107: 635 0.107 - 0.160: 247 0.160 - 0.213: 38 0.213 - 0.267: 9 Chirality restraints: 2520 Sorted by residual: chirality pdb=" CA ASN A 699 " pdb=" N ASN A 699 " pdb=" C ASN A 699 " pdb=" CB ASN A 699 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CA ASN D 699 " pdb=" N ASN D 699 " pdb=" C ASN D 699 " pdb=" CB ASN D 699 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA ARG F 248 " pdb=" N ARG F 248 " pdb=" C ARG F 248 " pdb=" CB ARG F 248 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 2517 not shown) Planarity restraints: 4944 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 500 " 0.754 9.50e-02 1.11e+02 2.52e-01 6.95e+01 pdb=" NE ARG A 500 " -0.024 2.00e-02 2.50e+03 pdb=" CZ ARG A 500 " -0.041 2.00e-02 2.50e+03 pdb=" NH1 ARG A 500 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 500 " 0.008 2.00e-02 2.50e+03 pdb="HH11 ARG A 500 " -0.006 2.00e-02 2.50e+03 pdb="HH12 ARG A 500 " 0.006 2.00e-02 2.50e+03 pdb="HH21 ARG A 500 " 0.004 2.00e-02 2.50e+03 pdb="HH22 ARG A 500 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 500 " -0.754 9.50e-02 1.11e+02 2.52e-01 6.95e+01 pdb=" NE ARG D 500 " 0.024 2.00e-02 2.50e+03 pdb=" CZ ARG D 500 " 0.041 2.00e-02 2.50e+03 pdb=" NH1 ARG D 500 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG D 500 " -0.008 2.00e-02 2.50e+03 pdb="HH11 ARG D 500 " 0.006 2.00e-02 2.50e+03 pdb="HH12 ARG D 500 " -0.006 2.00e-02 2.50e+03 pdb="HH21 ARG D 500 " -0.004 2.00e-02 2.50e+03 pdb="HH22 ARG D 500 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 734 " -0.380 9.50e-02 1.11e+02 1.27e-01 1.73e+01 pdb=" NE ARG A 734 " 0.020 2.00e-02 2.50e+03 pdb=" CZ ARG A 734 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 734 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 734 " -0.004 2.00e-02 2.50e+03 pdb="HH11 ARG A 734 " 0.006 2.00e-02 2.50e+03 pdb="HH12 ARG A 734 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG A 734 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 734 " -0.004 2.00e-02 2.50e+03 ... (remaining 4941 not shown) Histogram of nonbonded interaction distances: 1.22 - 1.90: 179 1.90 - 2.57: 31111 2.57 - 3.25: 104416 3.25 - 3.92: 126028 3.92 - 4.60: 201555 Nonbonded interactions: 463289 Sorted by model distance: nonbonded pdb=" OH TYR A 262 " pdb=" HZ3 LYS D 311 " model vdw 1.223 2.450 nonbonded pdb=" OH TYR A 262 " pdb=" HZ1 LYS D 311 " model vdw 1.543 2.450 nonbonded pdb=" OH TYR A 262 " pdb=" NZ LYS D 311 " model vdw 1.603 2.950 nonbonded pdb=" OE2 GLU A 130 " pdb=" HH TYR A 134 " model vdw 1.680 2.450 nonbonded pdb=" OE2 GLU D 130 " pdb=" HH TYR D 134 " model vdw 1.681 2.450 ... (remaining 463284 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.200 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 50.440 Find NCS groups from input model: 0.190 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:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5536 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 17104 Z= 0.313 Angle : 0.940 11.619 23112 Z= 0.534 Chirality : 0.065 0.267 2520 Planarity : 0.014 0.326 3002 Dihedral : 11.486 79.623 6542 Min Nonbonded Distance : 1.603 Molprobity Statistics. All-atom Clashscore : 1.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.27 % Allowed : 2.45 % Favored : 97.28 % 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: -0.72 (0.17), residues: 2034 helix: -0.79 (0.15), residues: 964 sheet: -0.26 (0.33), residues: 236 loop : 0.14 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG D 500 TYR 0.033 0.004 TYR A 494 PHE 0.043 0.004 PHE D 256 TRP 0.016 0.003 TRP D 791 HIS 0.011 0.002 HIS F 233 Details of bonding type rmsd covalent geometry : bond 0.00616 (17080) covalent geometry : angle 0.92106 (23082) hydrogen bonds : bond 0.13804 ( 844) hydrogen bonds : angle 7.32616 ( 2352) metal coordination : bond 0.02257 ( 24) metal coordination : angle 5.25689 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4068 Ramachandran restraints generated. 2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4068 Ramachandran restraints generated. 2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Residue MET 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Evaluate side-chains 473 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 468 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 550 ASP cc_start: 0.6743 (m-30) cc_final: 0.6196 (t70) REVERT: A 653 ASP cc_start: 0.7757 (m-30) cc_final: 0.7332 (t0) REVERT: A 680 PHE cc_start: 0.7671 (m-80) cc_final: 0.7322 (m-80) REVERT: B 59 ILE cc_start: 0.3210 (mm) cc_final: 0.2985 (mm) REVERT: C 169 MET cc_start: 0.6812 (mtp) cc_final: 0.6350 (ptm) REVERT: C 243 MET cc_start: 0.8235 (mtp) cc_final: 0.7879 (mpp) REVERT: D 488 THR cc_start: 0.8455 (m) cc_final: 0.8243 (p) REVERT: D 550 ASP cc_start: 0.7317 (m-30) cc_final: 0.6729 (t70) REVERT: D 680 PHE cc_start: 0.7316 (m-80) cc_final: 0.6862 (m-80) REVERT: E 109 ARG cc_start: 0.6837 (mtt-85) cc_final: 0.6624 (mmt90) REVERT: F 120 LYS cc_start: 0.4786 (tttt) cc_final: 0.4187 (pttt) REVERT: F 282 ARG cc_start: 0.6305 (ttt180) cc_final: 0.5858 (ttp80) REVERT: F 284 THR cc_start: 0.9173 (m) cc_final: 0.8810 (p) outliers start: 5 outliers final: 1 residues processed: 473 average time/residue: 0.3851 time to fit residues: 252.1735 Evaluate side-chains 266 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 265 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 503 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 30.0000 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 8.9990 chunk 200 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.0470 overall best weight: 2.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 21 GLN B 31 HIS B 98 GLN E 21 GLN E 98 GLN E 114 GLN F 131 ASN ** F 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 165 GLN F 167 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4820 r_free = 0.4820 target = 0.178348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.147093 restraints weight = 148751.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.152084 restraints weight = 79760.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.152674 restraints weight = 49360.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.153009 restraints weight = 47781.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.153612 restraints weight = 46069.282| |-----------------------------------------------------------------------------| r_work (final): 0.4464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6094 moved from start: 0.4171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17104 Z= 0.183 Angle : 0.650 10.454 23112 Z= 0.347 Chirality : 0.040 0.180 2520 Planarity : 0.005 0.083 3002 Dihedral : 4.550 33.512 2285 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.81 % Allowed : 8.09 % Favored : 90.10 % 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: 0.37 (0.18), residues: 2034 helix: 0.67 (0.16), residues: 968 sheet: -0.60 (0.33), residues: 240 loop : 0.22 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 181 TYR 0.020 0.002 TYR E 67 PHE 0.018 0.002 PHE B 52 TRP 0.013 0.002 TRP A 791 HIS 0.006 0.001 HIS B 85 Details of bonding type rmsd covalent geometry : bond 0.00397 (17080) covalent geometry : angle 0.63940 (23082) hydrogen bonds : bond 0.04838 ( 844) hydrogen bonds : angle 5.57872 ( 2352) metal coordination : bond 0.01454 ( 24) metal coordination : angle 3.28348 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4068 Ramachandran restraints generated. 2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4068 Ramachandran restraints generated. 2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Residue MET 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Evaluate side-chains 301 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 267 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 495 TYR cc_start: 0.7186 (OUTLIER) cc_final: 0.6513 (t80) REVERT: A 550 ASP cc_start: 0.7309 (m-30) cc_final: 0.6640 (t70) REVERT: A 680 PHE cc_start: 0.8398 (m-80) cc_final: 0.8073 (m-80) REVERT: A 693 MET cc_start: 0.6169 (mmp) cc_final: 0.5806 (mmm) REVERT: A 825 MET cc_start: 0.2693 (mtt) cc_final: 0.2175 (mtt) REVERT: B 79 LYS cc_start: 0.7717 (tptt) cc_final: 0.7164 (ttmt) REVERT: B 109 ARG cc_start: 0.6207 (mpt180) cc_final: 0.6002 (mpt180) REVERT: B 140 THR cc_start: 0.7161 (p) cc_final: 0.6882 (t) REVERT: C 165 GLN cc_start: 0.6837 (mt0) cc_final: 0.6623 (mp10) REVERT: C 167 GLN cc_start: 0.6892 (pt0) cc_final: 0.6554 (pm20) REVERT: C 243 MET cc_start: 0.8448 (mtp) cc_final: 0.7836 (mpp) REVERT: D 291 MET cc_start: 0.7505 (mmm) cc_final: 0.7184 (tpp) REVERT: D 313 MET cc_start: 0.8290 (ttm) cc_final: 0.7873 (ttm) REVERT: D 460 MET cc_start: 0.7679 (mmm) cc_final: 0.7219 (mmm) REVERT: D 488 THR cc_start: 0.8519 (m) cc_final: 0.8019 (p) REVERT: D 495 TYR cc_start: 0.7124 (OUTLIER) cc_final: 0.6754 (t80) REVERT: D 545 MET cc_start: 0.7459 (tpp) cc_final: 0.7127 (tpp) REVERT: D 550 ASP cc_start: 0.7669 (m-30) cc_final: 0.7192 (t70) REVERT: D 618 VAL cc_start: 0.7581 (t) cc_final: 0.7199 (p) REVERT: D 680 PHE cc_start: 0.7666 (m-80) cc_final: 0.7078 (m-80) REVERT: D 825 MET cc_start: 0.3346 (mtt) cc_final: 0.2982 (mtt) outliers start: 34 outliers final: 22 residues processed: 293 average time/residue: 0.3260 time to fit residues: 138.9838 Evaluate side-chains 244 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 220 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 490 ASN Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 115 LYS Chi-restraints excluded: chain C residue 204 GLU Chi-restraints excluded: chain C residue 239 ASN Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 495 TYR Chi-restraints excluded: chain D residue 522 TYR Chi-restraints excluded: chain D residue 653 ASP Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain F residue 233 HIS Chi-restraints excluded: chain F residue 255 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 93 optimal weight: 6.9990 chunk 192 optimal weight: 4.9990 chunk 203 optimal weight: 6.9990 chunk 117 optimal weight: 2.9990 chunk 53 optimal weight: 8.9990 chunk 167 optimal weight: 20.0000 chunk 113 optimal weight: 0.7980 chunk 180 optimal weight: 0.4980 chunk 46 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 169 optimal weight: 10.0000 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 288 ASN E 98 GLN ** F 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 288 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4758 r_free = 0.4758 target = 0.173888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.143108 restraints weight = 144273.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.145688 restraints weight = 80482.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.147197 restraints weight = 55031.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.147924 restraints weight = 49230.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.147830 restraints weight = 42500.594| |-----------------------------------------------------------------------------| r_work (final): 0.4361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6276 moved from start: 0.5474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17104 Z= 0.170 Angle : 0.591 6.298 23112 Z= 0.316 Chirality : 0.040 0.161 2520 Planarity : 0.005 0.049 3002 Dihedral : 4.267 19.254 2284 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.86 % Allowed : 9.48 % Favored : 88.66 % 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: 0.67 (0.19), residues: 2034 helix: 0.90 (0.16), residues: 986 sheet: -0.64 (0.33), residues: 240 loop : 0.45 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 529 TYR 0.022 0.002 TYR A 502 PHE 0.019 0.002 PHE D 612 TRP 0.013 0.002 TRP C 146 HIS 0.006 0.001 HIS D 531 Details of bonding type rmsd covalent geometry : bond 0.00371 (17080) covalent geometry : angle 0.58568 (23082) hydrogen bonds : bond 0.04448 ( 844) hydrogen bonds : angle 5.31108 ( 2352) metal coordination : bond 0.01390 ( 24) metal coordination : angle 2.23782 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4068 Ramachandran restraints generated. 2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4068 Ramachandran restraints generated. 2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Residue MET 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Evaluate side-chains 277 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 242 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7967 (tt) REVERT: A 440 ARG cc_start: 0.3198 (tpm170) cc_final: 0.2592 (tpt170) REVERT: A 476 SER cc_start: 0.8324 (t) cc_final: 0.7800 (m) REVERT: A 495 TYR cc_start: 0.7158 (OUTLIER) cc_final: 0.5941 (t80) REVERT: A 550 ASP cc_start: 0.7409 (m-30) cc_final: 0.7189 (t70) REVERT: A 573 GLU cc_start: 0.7942 (tt0) cc_final: 0.7407 (tp30) REVERT: A 635 MET cc_start: 0.7879 (mmp) cc_final: 0.7646 (mmp) REVERT: A 693 MET cc_start: 0.6494 (mmp) cc_final: 0.6266 (mmm) REVERT: A 825 MET cc_start: 0.3140 (mtt) cc_final: 0.2540 (mtt) REVERT: B 79 LYS cc_start: 0.7710 (tptt) cc_final: 0.7124 (ttmt) REVERT: B 109 ARG cc_start: 0.6307 (mpt180) cc_final: 0.5862 (mmt-90) REVERT: C 243 MET cc_start: 0.8356 (mtp) cc_final: 0.7720 (mpp) REVERT: D 313 MET cc_start: 0.8687 (ttm) cc_final: 0.8437 (ttm) REVERT: D 440 ARG cc_start: 0.2779 (tpm170) cc_final: 0.2185 (tpt170) REVERT: D 488 THR cc_start: 0.8423 (m) cc_final: 0.8069 (p) REVERT: D 495 TYR cc_start: 0.7164 (OUTLIER) cc_final: 0.6284 (t80) REVERT: D 618 VAL cc_start: 0.8010 (t) cc_final: 0.7673 (p) REVERT: D 635 MET cc_start: 0.7556 (mmp) cc_final: 0.7273 (mmp) REVERT: D 680 PHE cc_start: 0.7927 (m-80) cc_final: 0.7480 (m-80) REVERT: F 134 PHE cc_start: 0.4976 (m-80) cc_final: 0.4590 (m-80) outliers start: 35 outliers final: 20 residues processed: 265 average time/residue: 0.3767 time to fit residues: 140.3054 Evaluate side-chains 225 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 202 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 490 ASN Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 653 ASP Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 125 HIS Chi-restraints excluded: chain D residue 151 ARG Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 495 TYR Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 522 TYR Chi-restraints excluded: chain D residue 573 GLU Chi-restraints excluded: chain D residue 653 ASP Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain F residue 233 HIS Chi-restraints excluded: chain F residue 263 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 149 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 128 optimal weight: 0.6980 chunk 4 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 174 optimal weight: 6.9990 chunk 102 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN ** F 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4748 r_free = 0.4748 target = 0.172071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.141292 restraints weight = 144179.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.143861 restraints weight = 75764.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.145627 restraints weight = 52594.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.146105 restraints weight = 43234.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.146184 restraints weight = 40872.506| |-----------------------------------------------------------------------------| r_work (final): 0.4353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6341 moved from start: 0.6224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17104 Z= 0.137 Angle : 0.536 6.009 23112 Z= 0.282 Chirality : 0.038 0.162 2520 Planarity : 0.005 0.106 3002 Dihedral : 4.116 18.268 2284 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.02 % Allowed : 10.12 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.19), residues: 2034 helix: 1.13 (0.16), residues: 988 sheet: -0.59 (0.33), residues: 240 loop : 0.59 (0.23), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 245 TYR 0.015 0.001 TYR B 67 PHE 0.015 0.001 PHE A 612 TRP 0.010 0.002 TRP B 139 HIS 0.004 0.001 HIS E 125 Details of bonding type rmsd covalent geometry : bond 0.00297 (17080) covalent geometry : angle 0.53145 (23082) hydrogen bonds : bond 0.03780 ( 844) hydrogen bonds : angle 5.04638 ( 2352) metal coordination : bond 0.00829 ( 24) metal coordination : angle 1.94576 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4068 Ramachandran restraints generated. 2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4068 Ramachandran restraints generated. 2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Residue MET 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Evaluate side-chains 259 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 221 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7830 (tt) REVERT: A 236 ILE cc_start: 0.6782 (OUTLIER) cc_final: 0.6556 (mp) REVERT: A 304 MET cc_start: 0.8062 (tpp) cc_final: 0.7747 (tpp) REVERT: A 440 ARG cc_start: 0.3782 (tpm170) cc_final: 0.2832 (tpt170) REVERT: A 476 SER cc_start: 0.8199 (t) cc_final: 0.7641 (m) REVERT: A 495 TYR cc_start: 0.7153 (OUTLIER) cc_final: 0.6182 (t80) REVERT: A 550 ASP cc_start: 0.7685 (m-30) cc_final: 0.7219 (t70) REVERT: A 573 GLU cc_start: 0.7989 (tt0) cc_final: 0.7452 (tp30) REVERT: A 635 MET cc_start: 0.7890 (mmp) cc_final: 0.7656 (mmp) REVERT: A 680 PHE cc_start: 0.7556 (m-10) cc_final: 0.7171 (m-10) REVERT: A 693 MET cc_start: 0.6635 (mmp) cc_final: 0.6262 (mmm) REVERT: A 825 MET cc_start: 0.3024 (mtt) cc_final: 0.2633 (mtt) REVERT: B 109 ARG cc_start: 0.6242 (mpt180) cc_final: 0.5814 (mmt-90) REVERT: C 243 MET cc_start: 0.8480 (mtp) cc_final: 0.7763 (mpp) REVERT: D 313 MET cc_start: 0.8583 (ttm) cc_final: 0.8303 (ttm) REVERT: D 440 ARG cc_start: 0.2844 (tpm170) cc_final: 0.2624 (tpt170) REVERT: D 495 TYR cc_start: 0.7317 (OUTLIER) cc_final: 0.6387 (t80) REVERT: D 502 TYR cc_start: 0.7522 (t80) cc_final: 0.7219 (m-80) REVERT: D 511 TYR cc_start: 0.5608 (OUTLIER) cc_final: 0.3953 (m-80) REVERT: D 542 MET cc_start: 0.8205 (mmp) cc_final: 0.7527 (ptt) REVERT: D 618 VAL cc_start: 0.7979 (t) cc_final: 0.7685 (p) REVERT: D 680 PHE cc_start: 0.7983 (m-80) cc_final: 0.7525 (m-10) REVERT: F 134 PHE cc_start: 0.4865 (m-80) cc_final: 0.4097 (m-80) REVERT: F 237 MET cc_start: -0.2820 (OUTLIER) cc_final: -0.3423 (mmt) outliers start: 38 outliers final: 24 residues processed: 250 average time/residue: 0.3315 time to fit residues: 118.9052 Evaluate side-chains 222 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 192 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 243 TYR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 490 ASN Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 653 ASP Chi-restraints excluded: chain B residue 125 HIS Chi-restraints excluded: chain C residue 239 ASN Chi-restraints excluded: chain D residue 151 ARG Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 279 ARG Chi-restraints excluded: chain D residue 495 TYR Chi-restraints excluded: chain D residue 511 TYR Chi-restraints excluded: chain D residue 522 TYR Chi-restraints excluded: chain D residue 653 ASP Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain F residue 233 HIS Chi-restraints excluded: chain F residue 237 MET Chi-restraints excluded: chain F residue 239 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 110 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 129 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 203 optimal weight: 3.9990 chunk 198 optimal weight: 5.9990 chunk 164 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 188 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 186 optimal weight: 7.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4723 r_free = 0.4723 target = 0.170513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.139203 restraints weight = 143865.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.142076 restraints weight = 80087.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.142708 restraints weight = 54060.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.143445 restraints weight = 49799.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.143637 restraints weight = 44982.152| |-----------------------------------------------------------------------------| r_work (final): 0.4287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6451 moved from start: 0.6832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17104 Z= 0.151 Angle : 0.540 5.074 23112 Z= 0.287 Chirality : 0.038 0.151 2520 Planarity : 0.004 0.048 3002 Dihedral : 4.108 19.696 2284 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.97 % Allowed : 11.02 % Favored : 87.01 % 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 (0.19), residues: 2034 helix: 1.11 (0.16), residues: 988 sheet: -0.54 (0.33), residues: 240 loop : 0.49 (0.23), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 505 TYR 0.038 0.001 TYR D 502 PHE 0.015 0.002 PHE D 612 TRP 0.009 0.002 TRP E 139 HIS 0.006 0.001 HIS E 85 Details of bonding type rmsd covalent geometry : bond 0.00329 (17080) covalent geometry : angle 0.53433 (23082) hydrogen bonds : bond 0.03849 ( 844) hydrogen bonds : angle 5.04500 ( 2352) metal coordination : bond 0.01070 ( 24) metal coordination : angle 2.24424 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4068 Ramachandran restraints generated. 2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4068 Ramachandran restraints generated. 2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Residue MET 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Evaluate side-chains 246 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 209 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.7483 (OUTLIER) cc_final: 0.7106 (mmm160) REVERT: A 163 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.8005 (tt) REVERT: A 440 ARG cc_start: 0.4483 (tpm170) cc_final: 0.4246 (tpt170) REVERT: A 476 SER cc_start: 0.8334 (t) cc_final: 0.7853 (m) REVERT: A 495 TYR cc_start: 0.7133 (OUTLIER) cc_final: 0.6141 (t80) REVERT: A 511 TYR cc_start: 0.4815 (OUTLIER) cc_final: 0.1914 (m-80) REVERT: A 550 ASP cc_start: 0.7422 (m-30) cc_final: 0.7075 (t70) REVERT: A 635 MET cc_start: 0.7982 (mmp) cc_final: 0.7726 (mmp) REVERT: A 680 PHE cc_start: 0.7396 (m-10) cc_final: 0.7110 (m-10) REVERT: A 693 MET cc_start: 0.6643 (mmp) cc_final: 0.6339 (mmm) REVERT: A 825 MET cc_start: 0.3333 (mtt) cc_final: 0.3030 (mtt) REVERT: B 109 ARG cc_start: 0.6338 (mpt180) cc_final: 0.6043 (mmt-90) REVERT: C 243 MET cc_start: 0.8508 (mtp) cc_final: 0.7879 (mpp) REVERT: D 313 MET cc_start: 0.8738 (ttm) cc_final: 0.8476 (ttm) REVERT: D 431 GLU cc_start: 0.6172 (tm-30) cc_final: 0.5910 (tm-30) REVERT: D 495 TYR cc_start: 0.7294 (OUTLIER) cc_final: 0.6431 (t80) REVERT: D 511 TYR cc_start: 0.5413 (OUTLIER) cc_final: 0.3804 (m-80) REVERT: D 542 MET cc_start: 0.8407 (mmp) cc_final: 0.7574 (ptt) REVERT: D 550 ASP cc_start: 0.6780 (OUTLIER) cc_final: 0.6393 (t70) REVERT: D 618 VAL cc_start: 0.8143 (t) cc_final: 0.7846 (p) REVERT: D 680 PHE cc_start: 0.7941 (m-80) cc_final: 0.7458 (m-10) REVERT: F 237 MET cc_start: -0.1459 (OUTLIER) cc_final: -0.2193 (mmt) outliers start: 37 outliers final: 25 residues processed: 238 average time/residue: 0.3572 time to fit residues: 121.3750 Evaluate side-chains 221 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 188 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 243 TYR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 490 ASN Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 653 ASP Chi-restraints excluded: chain B residue 125 HIS Chi-restraints excluded: chain D residue 151 ARG Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 279 ARG Chi-restraints excluded: chain D residue 495 TYR Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 505 ARG Chi-restraints excluded: chain D residue 511 TYR Chi-restraints excluded: chain D residue 522 TYR Chi-restraints excluded: chain D residue 550 ASP Chi-restraints excluded: chain D residue 653 ASP Chi-restraints excluded: chain D residue 713 PHE Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain F residue 233 HIS Chi-restraints excluded: chain F residue 237 MET Chi-restraints excluded: chain F residue 239 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 157 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 181 optimal weight: 0.9990 chunk 52 optimal weight: 8.9990 chunk 134 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 148 optimal weight: 9.9990 chunk 188 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 625 ASN ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 497 ASN ** D 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 GLN ** F 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4691 r_free = 0.4691 target = 0.168374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.135354 restraints weight = 144076.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.138554 restraints weight = 83275.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.139257 restraints weight = 58406.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.140291 restraints weight = 49934.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.140299 restraints weight = 46151.896| |-----------------------------------------------------------------------------| r_work (final): 0.4236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6534 moved from start: 0.7408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17104 Z= 0.143 Angle : 0.532 5.349 23112 Z= 0.282 Chirality : 0.039 0.150 2520 Planarity : 0.004 0.048 3002 Dihedral : 4.060 18.665 2284 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.02 % Allowed : 11.40 % Favored : 86.58 % 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: 0.85 (0.19), residues: 2034 helix: 1.13 (0.16), residues: 988 sheet: -0.55 (0.33), residues: 240 loop : 0.41 (0.22), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 505 TYR 0.014 0.001 TYR B 67 PHE 0.013 0.001 PHE D 612 TRP 0.017 0.002 TRP B 139 HIS 0.004 0.001 HIS F 168 Details of bonding type rmsd covalent geometry : bond 0.00314 (17080) covalent geometry : angle 0.52762 (23082) hydrogen bonds : bond 0.03664 ( 844) hydrogen bonds : angle 4.96443 ( 2352) metal coordination : bond 0.01082 ( 24) metal coordination : angle 2.03797 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4068 Ramachandran restraints generated. 2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4068 Ramachandran restraints generated. 2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Residue MET 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Evaluate side-chains 240 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 202 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.7740 (OUTLIER) cc_final: 0.7147 (mmm160) REVERT: A 163 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.8043 (tt) REVERT: A 304 MET cc_start: 0.7699 (tpp) cc_final: 0.7487 (tpp) REVERT: A 377 MET cc_start: 0.8218 (tpp) cc_final: 0.7698 (ttt) REVERT: A 440 ARG cc_start: 0.4484 (tpm170) cc_final: 0.4237 (tpt170) REVERT: A 476 SER cc_start: 0.8069 (t) cc_final: 0.7745 (m) REVERT: A 495 TYR cc_start: 0.7164 (OUTLIER) cc_final: 0.6200 (t80) REVERT: A 550 ASP cc_start: 0.7626 (m-30) cc_final: 0.7403 (t70) REVERT: A 572 LYS cc_start: 0.8375 (tttt) cc_final: 0.7961 (tttt) REVERT: A 635 MET cc_start: 0.7868 (mmp) cc_final: 0.7533 (mmp) REVERT: A 680 PHE cc_start: 0.7358 (m-10) cc_final: 0.7051 (m-10) REVERT: A 825 MET cc_start: 0.3223 (mtt) cc_final: 0.2947 (mtt) REVERT: B 109 ARG cc_start: 0.6459 (mpt180) cc_final: 0.5763 (mmt90) REVERT: C 167 GLN cc_start: 0.7044 (pt0) cc_final: 0.6596 (pm20) REVERT: C 243 MET cc_start: 0.8645 (mtp) cc_final: 0.7947 (mpp) REVERT: D 313 MET cc_start: 0.8688 (ttm) cc_final: 0.8414 (ttm) REVERT: D 495 TYR cc_start: 0.7479 (OUTLIER) cc_final: 0.6594 (t80) REVERT: D 511 TYR cc_start: 0.5420 (OUTLIER) cc_final: 0.3456 (m-80) REVERT: D 542 MET cc_start: 0.8420 (mmp) cc_final: 0.7379 (ptt) REVERT: D 572 LYS cc_start: 0.7543 (tttt) cc_final: 0.7202 (mmtt) REVERT: D 618 VAL cc_start: 0.8118 (t) cc_final: 0.7696 (p) REVERT: D 680 PHE cc_start: 0.7970 (m-80) cc_final: 0.7535 (m-10) outliers start: 38 outliers final: 29 residues processed: 228 average time/residue: 0.3719 time to fit residues: 119.5526 Evaluate side-chains 221 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 187 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 243 TYR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 490 ASN Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 653 ASP Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 125 HIS Chi-restraints excluded: chain C residue 239 ASN Chi-restraints excluded: chain D residue 151 ARG Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 279 ARG Chi-restraints excluded: chain D residue 495 TYR Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 511 TYR Chi-restraints excluded: chain D residue 522 TYR Chi-restraints excluded: chain D residue 573 GLU Chi-restraints excluded: chain D residue 653 ASP Chi-restraints excluded: chain D residue 713 PHE Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain F residue 160 MET Chi-restraints excluded: chain F residue 233 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 35 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 175 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 HIS ** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 626 ASN ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 625 ASN ** F 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.166672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.133965 restraints weight = 143844.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.136077 restraints weight = 89098.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.136482 restraints weight = 62142.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.137540 restraints weight = 57092.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.137514 restraints weight = 50016.471| |-----------------------------------------------------------------------------| r_work (final): 0.4198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6594 moved from start: 0.7884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17104 Z= 0.144 Angle : 0.532 5.671 23112 Z= 0.280 Chirality : 0.038 0.150 2520 Planarity : 0.004 0.050 3002 Dihedral : 4.020 19.612 2284 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.92 % Allowed : 11.93 % Favored : 86.16 % 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: 0.88 (0.19), residues: 2034 helix: 1.24 (0.17), residues: 988 sheet: -0.59 (0.33), residues: 236 loop : 0.30 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 734 TYR 0.026 0.001 TYR E 83 PHE 0.028 0.002 PHE A 648 TRP 0.012 0.001 TRP B 139 HIS 0.004 0.001 HIS B 85 Details of bonding type rmsd covalent geometry : bond 0.00315 (17080) covalent geometry : angle 0.52422 (23082) hydrogen bonds : bond 0.03661 ( 844) hydrogen bonds : angle 4.99578 ( 2352) metal coordination : bond 0.01184 ( 24) metal coordination : angle 2.50449 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4068 Ramachandran restraints generated. 2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4068 Ramachandran restraints generated. 2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Residue MET 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Evaluate side-chains 227 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 191 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.7038 (mmm160) REVERT: A 339 MET cc_start: 0.7989 (mtt) cc_final: 0.7753 (mtt) REVERT: A 495 TYR cc_start: 0.7232 (OUTLIER) cc_final: 0.6387 (t80) REVERT: A 511 TYR cc_start: 0.5268 (OUTLIER) cc_final: 0.2455 (m-80) REVERT: A 635 MET cc_start: 0.7883 (mmp) cc_final: 0.7508 (mmp) REVERT: A 680 PHE cc_start: 0.7412 (m-10) cc_final: 0.7169 (m-10) REVERT: A 825 MET cc_start: 0.3274 (mtt) cc_final: 0.3018 (mtt) REVERT: B 109 ARG cc_start: 0.6503 (mpt180) cc_final: 0.5772 (mmt90) REVERT: C 160 MET cc_start: 0.4721 (mtm) cc_final: 0.4195 (mtp) REVERT: C 167 GLN cc_start: 0.7132 (pt0) cc_final: 0.6661 (pm20) REVERT: C 243 MET cc_start: 0.8646 (mtp) cc_final: 0.7945 (mpp) REVERT: D 313 MET cc_start: 0.8674 (ttm) cc_final: 0.8395 (ttm) REVERT: D 440 ARG cc_start: 0.3258 (tpm170) cc_final: 0.2822 (tpt170) REVERT: D 488 THR cc_start: 0.8413 (m) cc_final: 0.8066 (p) REVERT: D 495 TYR cc_start: 0.7350 (OUTLIER) cc_final: 0.6601 (t80) REVERT: D 511 TYR cc_start: 0.5424 (OUTLIER) cc_final: 0.3037 (m-80) REVERT: D 542 MET cc_start: 0.8583 (mmp) cc_final: 0.7368 (ptt) REVERT: D 550 ASP cc_start: 0.6950 (OUTLIER) cc_final: 0.6612 (t70) REVERT: D 618 VAL cc_start: 0.8231 (t) cc_final: 0.7801 (p) REVERT: D 642 MET cc_start: 0.8359 (mmm) cc_final: 0.8048 (mmm) REVERT: D 680 PHE cc_start: 0.7904 (m-80) cc_final: 0.7466 (m-10) REVERT: E 48 GLU cc_start: 0.8805 (mt-10) cc_final: 0.8166 (tp30) outliers start: 36 outliers final: 27 residues processed: 221 average time/residue: 0.3679 time to fit residues: 114.1115 Evaluate side-chains 215 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 182 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 243 TYR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 490 ASN Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 653 ASP Chi-restraints excluded: chain B residue 125 HIS Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain D residue 151 ARG Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 279 ARG Chi-restraints excluded: chain D residue 495 TYR Chi-restraints excluded: chain D residue 511 TYR Chi-restraints excluded: chain D residue 522 TYR Chi-restraints excluded: chain D residue 550 ASP Chi-restraints excluded: chain D residue 653 ASP Chi-restraints excluded: chain D residue 713 PHE Chi-restraints excluded: chain D residue 861 ARG Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain F residue 233 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 90 optimal weight: 10.0000 chunk 10 optimal weight: 0.4980 chunk 194 optimal weight: 3.9990 chunk 140 optimal weight: 5.9990 chunk 51 optimal weight: 20.0000 chunk 42 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 136 optimal weight: 6.9990 chunk 125 optimal weight: 0.0670 chunk 41 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 overall best weight: 2.3124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.163614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.129876 restraints weight = 143128.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.131968 restraints weight = 90169.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.133920 restraints weight = 61066.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.134857 restraints weight = 48043.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.134786 restraints weight = 45847.372| |-----------------------------------------------------------------------------| r_work (final): 0.4174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6646 moved from start: 0.8461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17104 Z= 0.176 Angle : 0.574 6.201 23112 Z= 0.306 Chirality : 0.039 0.160 2520 Planarity : 0.004 0.052 3002 Dihedral : 4.248 20.377 2284 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.13 % Allowed : 12.09 % Favored : 85.78 % 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: 0.54 (0.18), residues: 2034 helix: 0.98 (0.16), residues: 986 sheet: -0.64 (0.33), residues: 230 loop : 0.07 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 46 TYR 0.026 0.002 TYR E 83 PHE 0.013 0.002 PHE D 730 TRP 0.011 0.001 TRP B 139 HIS 0.005 0.001 HIS E 85 Details of bonding type rmsd covalent geometry : bond 0.00385 (17080) covalent geometry : angle 0.56640 (23082) hydrogen bonds : bond 0.04054 ( 844) hydrogen bonds : angle 5.15406 ( 2352) metal coordination : bond 0.01146 ( 24) metal coordination : angle 2.64003 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4068 Ramachandran restraints generated. 2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4068 Ramachandran restraints generated. 2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Residue MET 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Evaluate side-chains 232 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 192 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.7171 (mmm160) REVERT: A 339 MET cc_start: 0.8031 (mtt) cc_final: 0.7770 (mtt) REVERT: A 472 GLU cc_start: 0.7634 (tm-30) cc_final: 0.7345 (pm20) REVERT: A 495 TYR cc_start: 0.7388 (OUTLIER) cc_final: 0.6549 (t80) REVERT: A 511 TYR cc_start: 0.4896 (OUTLIER) cc_final: 0.2802 (m-80) REVERT: A 635 MET cc_start: 0.7921 (mmp) cc_final: 0.7545 (mmp) REVERT: A 825 MET cc_start: 0.3274 (mtt) cc_final: 0.3021 (mtt) REVERT: B 83 TYR cc_start: 0.8035 (m-10) cc_final: 0.7775 (m-10) REVERT: B 109 ARG cc_start: 0.6453 (mpt180) cc_final: 0.5752 (mmt90) REVERT: C 160 MET cc_start: 0.4876 (mtm) cc_final: 0.4333 (mtp) REVERT: C 243 MET cc_start: 0.8655 (mtp) cc_final: 0.7948 (mpp) REVERT: D 313 MET cc_start: 0.8702 (ttm) cc_final: 0.8471 (ttm) REVERT: D 476 SER cc_start: 0.8420 (t) cc_final: 0.8191 (m) REVERT: D 488 THR cc_start: 0.8564 (m) cc_final: 0.8189 (p) REVERT: D 495 TYR cc_start: 0.7144 (OUTLIER) cc_final: 0.6714 (t80) REVERT: D 511 TYR cc_start: 0.5349 (OUTLIER) cc_final: 0.2781 (m-80) REVERT: D 542 MET cc_start: 0.8669 (mmp) cc_final: 0.7391 (ptt) REVERT: D 680 PHE cc_start: 0.8023 (m-80) cc_final: 0.7547 (m-10) REVERT: D 825 MET cc_start: 0.3459 (mtt) cc_final: 0.2954 (mtt) outliers start: 40 outliers final: 31 residues processed: 221 average time/residue: 0.3823 time to fit residues: 117.9095 Evaluate side-chains 215 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 179 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 243 TYR Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 490 ASN Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 653 ASP Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 125 HIS Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 239 ASN Chi-restraints excluded: chain D residue 151 ARG Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 269 CYS Chi-restraints excluded: chain D residue 279 ARG Chi-restraints excluded: chain D residue 495 TYR Chi-restraints excluded: chain D residue 511 TYR Chi-restraints excluded: chain D residue 522 TYR Chi-restraints excluded: chain D residue 573 GLU Chi-restraints excluded: chain D residue 653 ASP Chi-restraints excluded: chain D residue 713 PHE Chi-restraints excluded: chain D residue 861 ARG Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain F residue 160 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 133 optimal weight: 4.9990 chunk 47 optimal weight: 7.9990 chunk 168 optimal weight: 20.0000 chunk 34 optimal weight: 3.9990 chunk 184 optimal weight: 10.0000 chunk 51 optimal weight: 20.0000 chunk 24 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 177 optimal weight: 0.8980 chunk 143 optimal weight: 0.8980 chunk 191 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 167 GLN ** D 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.163001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.130523 restraints weight = 143043.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.131759 restraints weight = 89026.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.132789 restraints weight = 63007.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.133329 restraints weight = 55467.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.133535 restraints weight = 49938.578| |-----------------------------------------------------------------------------| r_work (final): 0.4155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6682 moved from start: 0.8788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17104 Z= 0.162 Angle : 0.564 12.664 23112 Z= 0.296 Chirality : 0.039 0.151 2520 Planarity : 0.004 0.052 3002 Dihedral : 4.193 20.112 2284 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.08 % Allowed : 12.94 % Favored : 84.98 % 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: 0.55 (0.19), residues: 2034 helix: 1.06 (0.16), residues: 974 sheet: -0.76 (0.33), residues: 230 loop : 0.02 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 15 TYR 0.013 0.001 TYR F 205 PHE 0.018 0.002 PHE A 648 TRP 0.009 0.001 TRP E 139 HIS 0.006 0.001 HIS B 85 Details of bonding type rmsd covalent geometry : bond 0.00358 (17080) covalent geometry : angle 0.55681 (23082) hydrogen bonds : bond 0.03842 ( 844) hydrogen bonds : angle 5.09991 ( 2352) metal coordination : bond 0.00982 ( 24) metal coordination : angle 2.63495 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4068 Ramachandran restraints generated. 2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4068 Ramachandran restraints generated. 2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Residue MET 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Evaluate side-chains 228 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 189 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 MET cc_start: 0.8065 (mtt) cc_final: 0.7794 (mtt) REVERT: A 472 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7555 (pm20) REVERT: A 495 TYR cc_start: 0.7098 (OUTLIER) cc_final: 0.6568 (t80) REVERT: A 511 TYR cc_start: 0.5193 (OUTLIER) cc_final: 0.2341 (m-80) REVERT: A 635 MET cc_start: 0.7824 (mmp) cc_final: 0.7454 (mmp) REVERT: A 680 PHE cc_start: 0.7326 (m-80) cc_final: 0.7023 (m-10) REVERT: A 825 MET cc_start: 0.3236 (mtt) cc_final: 0.2997 (mtt) REVERT: B 83 TYR cc_start: 0.7816 (m-10) cc_final: 0.7602 (m-10) REVERT: B 109 ARG cc_start: 0.6611 (mpt180) cc_final: 0.5742 (mmt90) REVERT: C 160 MET cc_start: 0.4923 (mtm) cc_final: 0.4362 (mtp) REVERT: C 243 MET cc_start: 0.8650 (mtp) cc_final: 0.7944 (mpp) REVERT: D 313 MET cc_start: 0.8726 (ttm) cc_final: 0.8478 (ttm) REVERT: D 440 ARG cc_start: 0.3186 (tpm170) cc_final: 0.2755 (tpt170) REVERT: D 488 THR cc_start: 0.7896 (m) cc_final: 0.7513 (p) REVERT: D 495 TYR cc_start: 0.7233 (OUTLIER) cc_final: 0.6820 (t80) REVERT: D 511 TYR cc_start: 0.5302 (OUTLIER) cc_final: 0.2764 (m-80) REVERT: D 542 MET cc_start: 0.8767 (mmp) cc_final: 0.7527 (ptt) REVERT: D 550 ASP cc_start: 0.7001 (OUTLIER) cc_final: 0.6715 (t70) REVERT: D 618 VAL cc_start: 0.8328 (t) cc_final: 0.7905 (p) REVERT: D 680 PHE cc_start: 0.7911 (m-80) cc_final: 0.7430 (m-10) REVERT: D 825 MET cc_start: 0.3609 (mtt) cc_final: 0.3167 (mtt) REVERT: E 48 GLU cc_start: 0.8694 (mt-10) cc_final: 0.8279 (tp30) REVERT: F 134 PHE cc_start: 0.5462 (m-80) cc_final: 0.4111 (m-80) REVERT: F 288 ASN cc_start: 0.7773 (m110) cc_final: 0.7568 (m110) outliers start: 39 outliers final: 29 residues processed: 218 average time/residue: 0.3885 time to fit residues: 117.9826 Evaluate side-chains 213 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 179 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 243 TYR Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 490 ASN Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 653 ASP Chi-restraints excluded: chain B residue 125 HIS Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain D residue 151 ARG Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 495 TYR Chi-restraints excluded: chain D residue 511 TYR Chi-restraints excluded: chain D residue 522 TYR Chi-restraints excluded: chain D residue 550 ASP Chi-restraints excluded: chain D residue 573 GLU Chi-restraints excluded: chain D residue 648 PHE Chi-restraints excluded: chain D residue 653 ASP Chi-restraints excluded: chain D residue 713 PHE Chi-restraints excluded: chain D residue 861 ARG Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain F residue 160 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 69 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 131 optimal weight: 0.5980 chunk 180 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 146 optimal weight: 0.9980 chunk 103 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 ASN ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 497 ASN D 626 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.165562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.133779 restraints weight = 143513.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.135129 restraints weight = 87263.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.136271 restraints weight = 57209.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.136861 restraints weight = 53030.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.137008 restraints weight = 47110.112| |-----------------------------------------------------------------------------| r_work (final): 0.4199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6602 moved from start: 0.8842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17104 Z= 0.107 Angle : 0.519 8.082 23112 Z= 0.267 Chirality : 0.038 0.147 2520 Planarity : 0.004 0.059 3002 Dihedral : 3.943 18.837 2284 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.54 % Allowed : 13.58 % Favored : 84.88 % 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: 0.92 (0.19), residues: 2034 helix: 1.31 (0.17), residues: 990 sheet: -0.66 (0.33), residues: 230 loop : 0.30 (0.22), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 505 TYR 0.012 0.001 TYR E 83 PHE 0.015 0.001 PHE A 648 TRP 0.010 0.001 TRP E 139 HIS 0.002 0.000 HIS B 85 Details of bonding type rmsd covalent geometry : bond 0.00241 (17080) covalent geometry : angle 0.51298 (23082) hydrogen bonds : bond 0.03399 ( 844) hydrogen bonds : angle 4.82791 ( 2352) metal coordination : bond 0.00571 ( 24) metal coordination : angle 2.21982 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4068 Ramachandran restraints generated. 2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4068 Ramachandran restraints generated. 2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Residue MET 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Evaluate side-chains 227 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 198 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 MET cc_start: 0.8253 (tpp) cc_final: 0.7412 (ttt) REVERT: A 472 GLU cc_start: 0.7837 (tm-30) cc_final: 0.7572 (pm20) REVERT: A 495 TYR cc_start: 0.7006 (OUTLIER) cc_final: 0.6501 (t80) REVERT: A 511 TYR cc_start: 0.5154 (OUTLIER) cc_final: 0.2289 (m-80) REVERT: A 635 MET cc_start: 0.7561 (mmp) cc_final: 0.7341 (mmp) REVERT: A 680 PHE cc_start: 0.7286 (m-80) cc_final: 0.6984 (m-10) REVERT: A 825 MET cc_start: 0.3138 (mtt) cc_final: 0.2891 (mtt) REVERT: B 48 GLU cc_start: 0.8820 (mt-10) cc_final: 0.8121 (tp30) REVERT: B 109 ARG cc_start: 0.6647 (mpt180) cc_final: 0.5934 (mmt90) REVERT: C 243 MET cc_start: 0.8636 (mtp) cc_final: 0.7924 (mpp) REVERT: D 313 MET cc_start: 0.8624 (ttm) cc_final: 0.8318 (ttm) REVERT: D 440 ARG cc_start: 0.3033 (tpm170) cc_final: 0.2632 (tpt170) REVERT: D 488 THR cc_start: 0.8139 (m) cc_final: 0.7773 (p) REVERT: D 495 TYR cc_start: 0.7172 (OUTLIER) cc_final: 0.6783 (t80) REVERT: D 511 TYR cc_start: 0.5260 (OUTLIER) cc_final: 0.2901 (m-80) REVERT: D 542 MET cc_start: 0.8778 (mmp) cc_final: 0.7600 (ptt) REVERT: D 550 ASP cc_start: 0.6841 (OUTLIER) cc_final: 0.6315 (t70) REVERT: D 618 VAL cc_start: 0.8411 (t) cc_final: 0.7984 (p) REVERT: D 642 MET cc_start: 0.8286 (mmm) cc_final: 0.8014 (mmm) REVERT: D 680 PHE cc_start: 0.8019 (m-80) cc_final: 0.7565 (m-10) REVERT: D 825 MET cc_start: 0.3537 (mtt) cc_final: 0.3099 (mtt) REVERT: E 46 ARG cc_start: 0.8276 (ttp-110) cc_final: 0.7675 (tpp80) REVERT: E 48 GLU cc_start: 0.8711 (mt-10) cc_final: 0.8287 (tp30) REVERT: F 288 ASN cc_start: 0.7709 (m110) cc_final: 0.7508 (m110) outliers start: 29 outliers final: 21 residues processed: 218 average time/residue: 0.3557 time to fit residues: 110.1242 Evaluate side-chains 215 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 189 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 243 TYR Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 490 ASN Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 653 ASP Chi-restraints excluded: chain B residue 125 HIS Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain D residue 151 ARG Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 495 TYR Chi-restraints excluded: chain D residue 497 ASN Chi-restraints excluded: chain D residue 511 TYR Chi-restraints excluded: chain D residue 522 TYR Chi-restraints excluded: chain D residue 550 ASP Chi-restraints excluded: chain D residue 653 ASP Chi-restraints excluded: chain D residue 713 PHE Chi-restraints excluded: chain D residue 861 ARG Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain F residue 160 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 55 optimal weight: 2.9990 chunk 66 optimal weight: 30.0000 chunk 134 optimal weight: 7.9990 chunk 58 optimal weight: 10.0000 chunk 75 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 chunk 201 optimal weight: 10.0000 chunk 171 optimal weight: 0.4980 chunk 16 optimal weight: 4.9990 chunk 45 optimal weight: 0.5980 chunk 199 optimal weight: 10.0000 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 497 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4664 r_free = 0.4664 target = 0.165901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.134070 restraints weight = 145066.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.135855 restraints weight = 90132.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.135866 restraints weight = 65558.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.136690 restraints weight = 59315.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.136960 restraints weight = 51085.672| |-----------------------------------------------------------------------------| r_work (final): 0.4190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6619 moved from start: 0.8872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.252 17104 Z= 0.179 Angle : 0.723 59.173 23112 Z= 0.438 Chirality : 0.039 0.297 2520 Planarity : 0.004 0.056 3002 Dihedral : 3.947 18.790 2284 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.49 % Allowed : 13.47 % Favored : 85.04 % Cbeta Deviations : 0.05 % 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: 0.93 (0.19), residues: 2034 helix: 1.32 (0.17), residues: 990 sheet: -0.66 (0.33), residues: 230 loop : 0.31 (0.22), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 505 TYR 0.060 0.001 TYR D 243 PHE 0.014 0.001 PHE A 648 TRP 0.009 0.001 TRP E 139 HIS 0.002 0.000 HIS B 85 Details of bonding type rmsd covalent geometry : bond 0.00389 (17080) covalent geometry : angle 0.71907 (23082) hydrogen bonds : bond 0.03466 ( 844) hydrogen bonds : angle 4.83665 ( 2352) metal coordination : bond 0.00578 ( 24) metal coordination : angle 2.22089 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5258.09 seconds wall clock time: 90 minutes 20.31 seconds (5420.31 seconds total)