Starting phenix.real_space_refine on Sat Jun 28 16:36:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r1g_18810/06_2025/8r1g_18810.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r1g_18810/06_2025/8r1g_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_18810/06_2025/8r1g_18810.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r1g_18810/06_2025/8r1g_18810.map" model { file = "/net/cci-nas-00/data/ceres_data/8r1g_18810/06_2025/8r1g_18810.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r1g_18810/06_2025/8r1g_18810.cif" } resolution = 3.99 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: F, D, E Time building chain proxies: 39.44, per 1000 atoms: 1.19 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: 7.65 Conformation dependent library (CDL) restraints added in 2.2 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: 2.58 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: 12.08 Time building geometry restraints manager: 9.45 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: 0.09 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'F' } ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } 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: 0.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.490 Extract box with map and model: 1.090 Check model and map are aligned: 0.230 Set scattering table: 0.330 Process input model: 100.750 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.270 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.016 0.003 TRP D 791 HIS 0.011 0.002 HIS F 233 PHE 0.043 0.004 PHE D 256 TYR 0.033 0.004 TYR A 494 ARG 0.028 0.001 ARG D 500 Details of bonding type rmsd hydrogen bonds : bond 0.13804 ( 844) hydrogen bonds : angle 7.32616 ( 2352) metal coordination : bond 0.02257 ( 24) metal coordination : angle 5.25689 ( 30) covalent geometry : bond 0.00616 (17080) covalent geometry : angle 0.92106 (23082) *********************** 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 : 2.577 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 550 ASP cc_start: 0.6749 (m-30) cc_final: 0.6200 (t70) REVERT: A 653 ASP cc_start: 0.7762 (m-30) cc_final: 0.7334 (t0) REVERT: A 680 PHE cc_start: 0.7664 (m-80) cc_final: 0.7319 (m-80) REVERT: B 59 ILE cc_start: 0.3204 (mm) cc_final: 0.2981 (mm) REVERT: C 169 MET cc_start: 0.6798 (mtp) cc_final: 0.6353 (ptm) REVERT: C 243 MET cc_start: 0.8231 (mtp) cc_final: 0.7880 (mpp) REVERT: D 488 THR cc_start: 0.8454 (m) cc_final: 0.8248 (p) REVERT: D 550 ASP cc_start: 0.7314 (m-30) cc_final: 0.6728 (t70) REVERT: D 680 PHE cc_start: 0.7344 (m-80) cc_final: 0.6884 (m-80) REVERT: E 109 ARG cc_start: 0.6837 (mtt-85) cc_final: 0.6627 (mmt90) REVERT: F 120 LYS cc_start: 0.4774 (tttt) cc_final: 0.4177 (pttt) REVERT: F 282 ARG cc_start: 0.6301 (ttt180) cc_final: 0.5839 (ttp80) REVERT: F 284 THR cc_start: 0.9170 (m) cc_final: 0.8813 (p) outliers start: 5 outliers final: 1 residues processed: 473 average time/residue: 0.8206 time to fit residues: 538.5246 Evaluate side-chains 272 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 271 time to evaluate : 2.697 ------------------------------------------------------------------------------- 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 172 optimal weight: 1.9990 chunk 154 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 159 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 chunk 119 optimal weight: 0.8980 chunk 185 optimal weight: 9.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 31 HIS B 98 GLN ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 795 HIS E 21 GLN E 98 GLN E 114 GLN F 131 ASN ** F 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 167 GLN F 288 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4779 r_free = 0.4779 target = 0.174921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.140768 restraints weight = 147001.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.145446 restraints weight = 77962.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.148796 restraints weight = 53016.220| |-----------------------------------------------------------------------------| r_work (final): 0.4416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6196 moved from start: 0.4624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 17104 Z= 0.233 Angle : 0.706 12.288 23112 Z= 0.382 Chirality : 0.042 0.181 2520 Planarity : 0.006 0.079 3002 Dihedral : 4.760 37.899 2285 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.40 % Allowed : 8.04 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.18), residues: 2034 helix: 0.31 (0.16), residues: 980 sheet: -0.70 (0.34), residues: 234 loop : 0.13 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 791 HIS 0.007 0.002 HIS B 85 PHE 0.026 0.002 PHE B 52 TYR 0.028 0.002 TYR B 67 ARG 0.007 0.001 ARG D 155 Details of bonding type rmsd hydrogen bonds : bond 0.05312 ( 844) hydrogen bonds : angle 5.80222 ( 2352) metal coordination : bond 0.02293 ( 24) metal coordination : angle 3.65599 ( 30) covalent geometry : bond 0.00497 (17080) covalent geometry : angle 0.69438 (23082) *********************** 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 316 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 271 time to evaluate : 2.784 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: A 495 TYR cc_start: 0.7141 (OUTLIER) cc_final: 0.6178 (t80) REVERT: A 545 MET cc_start: 0.6719 (tpp) cc_final: 0.6346 (tpp) REVERT: A 680 PHE cc_start: 0.8058 (m-80) cc_final: 0.7848 (m-80) REVERT: A 693 MET cc_start: 0.5686 (mmp) cc_final: 0.5394 (mmm) REVERT: A 825 MET cc_start: 0.2767 (mtt) cc_final: 0.2309 (mtt) REVERT: B 79 LYS cc_start: 0.7780 (tptt) cc_final: 0.7134 (ttmt) REVERT: C 243 MET cc_start: 0.8059 (mtp) cc_final: 0.7660 (mpp) REVERT: D 291 MET cc_start: 0.7741 (mmm) cc_final: 0.7368 (tpp) REVERT: D 313 MET cc_start: 0.8762 (ttm) cc_final: 0.8462 (ttm) REVERT: D 339 MET cc_start: 0.7158 (mtm) cc_final: 0.6947 (mtt) REVERT: D 395 GLU cc_start: 0.6174 (mt-10) cc_final: 0.5904 (mp0) REVERT: D 488 THR cc_start: 0.8667 (m) cc_final: 0.8374 (p) REVERT: D 495 TYR cc_start: 0.7105 (OUTLIER) cc_final: 0.6404 (t80) REVERT: D 501 MET cc_start: 0.8412 (mtt) cc_final: 0.7685 (tmm) REVERT: D 540 LEU cc_start: 0.7517 (mt) cc_final: 0.7253 (mm) REVERT: D 550 ASP cc_start: 0.7565 (m-30) cc_final: 0.7240 (t70) REVERT: D 618 VAL cc_start: 0.7943 (t) cc_final: 0.7508 (p) REVERT: D 680 PHE cc_start: 0.7586 (m-80) cc_final: 0.7068 (m-80) REVERT: D 825 MET cc_start: 0.3406 (mtt) cc_final: 0.3080 (mtt) REVERT: F 120 LYS cc_start: 0.4364 (tttt) cc_final: 0.3974 (mtmt) REVERT: F 134 PHE cc_start: 0.4865 (m-80) cc_final: 0.4559 (m-80) REVERT: F 282 ARG cc_start: 0.6504 (ttt180) cc_final: 0.6195 (ttt180) outliers start: 45 outliers final: 28 residues processed: 302 average time/residue: 0.7110 time to fit residues: 314.6985 Evaluate side-chains 258 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 228 time to evaluate : 2.707 ------------------------------------------------------------------------------- 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 69 VAL Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 125 HIS 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 377 MET 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 653 ASP Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 233 HIS Chi-restraints excluded: chain F residue 263 ASN Chi-restraints excluded: chain F residue 289 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 163 optimal weight: 10.0000 chunk 110 optimal weight: 7.9990 chunk 167 optimal weight: 30.0000 chunk 29 optimal weight: 1.9990 chunk 98 optimal weight: 7.9990 chunk 178 optimal weight: 4.9990 chunk 33 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 137 optimal weight: 0.9990 chunk 187 optimal weight: 7.9990 chunk 179 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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** A 625 ASN ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 ASN D 258 ASN ** E 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN F 104 GLN ** F 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 165 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4743 r_free = 0.4743 target = 0.171862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.141129 restraints weight = 144099.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.143177 restraints weight = 81752.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.144732 restraints weight = 55480.262| |-----------------------------------------------------------------------------| r_work (final): 0.4318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6367 moved from start: 0.5781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17104 Z= 0.173 Angle : 0.598 5.123 23112 Z= 0.321 Chirality : 0.040 0.175 2520 Planarity : 0.005 0.043 3002 Dihedral : 4.449 34.879 2285 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.24 % Allowed : 9.96 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.19), residues: 2034 helix: 0.85 (0.16), residues: 984 sheet: -0.76 (0.33), residues: 240 loop : 0.35 (0.23), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 146 HIS 0.006 0.001 HIS E 31 PHE 0.019 0.002 PHE E 76 TYR 0.022 0.002 TYR A 502 ARG 0.008 0.001 ARG D 529 Details of bonding type rmsd hydrogen bonds : bond 0.04444 ( 844) hydrogen bonds : angle 5.30954 ( 2352) metal coordination : bond 0.01426 ( 24) metal coordination : angle 2.26570 ( 30) covalent geometry : bond 0.00375 (17080) covalent geometry : angle 0.59286 (23082) *********************** 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 281 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 239 time to evaluate : 2.677 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 163 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7966 (tt) REVERT: A 476 SER cc_start: 0.8441 (t) cc_final: 0.7929 (m) REVERT: A 495 TYR cc_start: 0.7197 (OUTLIER) cc_final: 0.6027 (t80) REVERT: A 545 MET cc_start: 0.6279 (tpp) cc_final: 0.5982 (tpp) REVERT: A 693 MET cc_start: 0.6622 (mmp) cc_final: 0.6408 (mmm) REVERT: A 825 MET cc_start: 0.3154 (mtt) cc_final: 0.2612 (mtt) REVERT: B 109 ARG cc_start: 0.6546 (mpt180) cc_final: 0.6089 (mmt-90) REVERT: C 243 MET cc_start: 0.8380 (mtp) cc_final: 0.7712 (mpp) REVERT: D 163 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8464 (tt) REVERT: D 313 MET cc_start: 0.8651 (ttm) cc_final: 0.8362 (ttm) REVERT: D 339 MET cc_start: 0.7607 (mtm) cc_final: 0.7292 (mtt) REVERT: D 431 GLU cc_start: 0.6197 (tm-30) cc_final: 0.5881 (tm-30) REVERT: D 488 THR cc_start: 0.8356 (m) cc_final: 0.8018 (p) REVERT: D 495 TYR cc_start: 0.7234 (OUTLIER) cc_final: 0.6282 (t80) REVERT: D 542 MET cc_start: 0.8120 (mmp) cc_final: 0.7509 (ptm) REVERT: D 550 ASP cc_start: 0.7605 (m-30) cc_final: 0.7256 (t70) REVERT: D 618 VAL cc_start: 0.8140 (t) cc_final: 0.7812 (p) REVERT: D 680 PHE cc_start: 0.8009 (m-80) cc_final: 0.7603 (m-80) REVERT: F 120 LYS cc_start: 0.4718 (tttt) cc_final: 0.4319 (mtmt) REVERT: F 134 PHE cc_start: 0.5202 (m-80) cc_final: 0.4224 (m-80) outliers start: 42 outliers final: 20 residues processed: 267 average time/residue: 0.8069 time to fit residues: 305.5116 Evaluate side-chains 229 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 205 time to evaluate : 2.666 ------------------------------------------------------------------------------- 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 325 ILE Chi-restraints excluded: chain A residue 480 CYS 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 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 158 SER Chi-restraints excluded: chain D residue 163 LEU 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 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 239 ASN Chi-restraints excluded: chain F residue 263 ASN Chi-restraints excluded: chain F residue 289 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 37 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 52 optimal weight: 8.9990 chunk 109 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 137 optimal weight: 0.3980 chunk 122 optimal weight: 4.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 ASN ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 626 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4724 r_free = 0.4724 target = 0.170076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.138624 restraints weight = 143497.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.141180 restraints weight = 79455.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.142553 restraints weight = 56433.225| |-----------------------------------------------------------------------------| r_work (final): 0.4285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6451 moved from start: 0.6578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17104 Z= 0.155 Angle : 0.562 5.807 23112 Z= 0.297 Chirality : 0.039 0.157 2520 Planarity : 0.004 0.046 3002 Dihedral : 4.350 32.713 2285 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.97 % Allowed : 11.08 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.19), residues: 2034 helix: 0.91 (0.16), residues: 986 sheet: -0.71 (0.33), residues: 240 loop : 0.35 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 139 HIS 0.004 0.001 HIS B 85 PHE 0.016 0.002 PHE B 76 TYR 0.017 0.001 TYR B 83 ARG 0.005 0.001 ARG A 505 Details of bonding type rmsd hydrogen bonds : bond 0.04012 ( 844) hydrogen bonds : angle 5.14998 ( 2352) metal coordination : bond 0.01063 ( 24) metal coordination : angle 2.25572 ( 30) covalent geometry : bond 0.00336 (17080) covalent geometry : angle 0.55677 (23082) *********************** 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 262 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 225 time to evaluate : 2.470 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: 0.8217 (OUTLIER) cc_final: 0.7963 (tt) REVERT: A 476 SER cc_start: 0.8507 (t) cc_final: 0.7964 (m) REVERT: A 495 TYR cc_start: 0.7094 (OUTLIER) cc_final: 0.6139 (t80) REVERT: A 511 TYR cc_start: 0.4667 (OUTLIER) cc_final: 0.1875 (m-80) REVERT: A 542 MET cc_start: 0.6554 (ptt) cc_final: 0.6145 (ptm) REVERT: A 693 MET cc_start: 0.6739 (mmp) cc_final: 0.6380 (mmm) REVERT: A 825 MET cc_start: 0.3134 (mtt) cc_final: 0.2770 (mtt) REVERT: B 99 TYR cc_start: 0.7106 (m-80) cc_final: 0.6875 (m-80) REVERT: B 109 ARG cc_start: 0.6561 (mpt180) cc_final: 0.6196 (mmt-90) REVERT: C 243 MET cc_start: 0.8506 (mtp) cc_final: 0.7836 (mpp) REVERT: D 313 MET cc_start: 0.8740 (ttm) cc_final: 0.8474 (ttm) REVERT: D 339 MET cc_start: 0.7563 (mtm) cc_final: 0.7227 (mtt) REVERT: D 488 THR cc_start: 0.8414 (m) cc_final: 0.8085 (p) REVERT: D 495 TYR cc_start: 0.7253 (OUTLIER) cc_final: 0.6408 (t80) REVERT: D 511 TYR cc_start: 0.5344 (OUTLIER) cc_final: 0.3642 (m-80) REVERT: D 542 MET cc_start: 0.8188 (mmp) cc_final: 0.7411 (ptm) REVERT: D 550 ASP cc_start: 0.7773 (m-30) cc_final: 0.7517 (t70) REVERT: D 618 VAL cc_start: 0.8138 (t) cc_final: 0.7848 (p) REVERT: D 642 MET cc_start: 0.8838 (mmt) cc_final: 0.8590 (mmm) REVERT: D 680 PHE cc_start: 0.8099 (m-80) cc_final: 0.7699 (m-80) REVERT: F 120 LYS cc_start: 0.4526 (tttt) cc_final: 0.4026 (mtmt) outliers start: 37 outliers final: 27 residues processed: 253 average time/residue: 0.8058 time to fit residues: 287.4766 Evaluate side-chains 238 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 206 time to evaluate : 2.494 ------------------------------------------------------------------------------- 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 236 ILE 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 497 ASN 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 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 395 GLU 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 27 GLN 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 Chi-restraints excluded: chain F residue 239 ASN Chi-restraints excluded: chain F residue 289 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 154 optimal weight: 7.9990 chunk 152 optimal weight: 8.9990 chunk 60 optimal weight: 40.0000 chunk 5 optimal weight: 0.7980 chunk 102 optimal weight: 7.9990 chunk 49 optimal weight: 8.9990 chunk 3 optimal weight: 4.9990 chunk 99 optimal weight: 9.9990 chunk 178 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 197 optimal weight: 10.0000 overall best weight: 4.9588 ------------------------------------------------------------------------------- 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** ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 ASN ** D 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN F 100 GLN F 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.160478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.128679 restraints weight = 144716.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.129109 restraints weight = 102010.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.130056 restraints weight = 76941.484| |-----------------------------------------------------------------------------| r_work (final): 0.4090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6819 moved from start: 0.8274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.070 17104 Z= 0.351 Angle : 0.807 9.851 23112 Z= 0.448 Chirality : 0.044 0.165 2520 Planarity : 0.007 0.082 3002 Dihedral : 5.386 24.613 2284 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.65 % Favored : 94.20 % Rotamer: Outliers : 3.25 % Allowed : 11.66 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.17), residues: 2034 helix: -0.39 (0.15), residues: 970 sheet: -0.90 (0.34), residues: 216 loop : -0.72 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 791 HIS 0.011 0.002 HIS B 85 PHE 0.026 0.003 PHE D 633 TYR 0.054 0.003 TYR D 134 ARG 0.010 0.001 ARG A 498 Details of bonding type rmsd hydrogen bonds : bond 0.06029 ( 844) hydrogen bonds : angle 6.26088 ( 2352) metal coordination : bond 0.02446 ( 24) metal coordination : angle 4.24175 ( 30) covalent geometry : bond 0.00759 (17080) covalent geometry : angle 0.79341 (23082) *********************** 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 274 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 213 time to evaluate : 2.500 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: A 163 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8340 (tt) REVERT: A 339 MET cc_start: 0.7958 (mtt) cc_final: 0.7749 (mtt) REVERT: A 340 MET cc_start: 0.8977 (tmm) cc_final: 0.8652 (tmm) REVERT: A 478 MET cc_start: 0.8240 (mtp) cc_final: 0.8015 (mtp) REVERT: A 495 TYR cc_start: 0.7387 (OUTLIER) cc_final: 0.6420 (t80) REVERT: A 511 TYR cc_start: 0.5205 (OUTLIER) cc_final: 0.3184 (m-80) REVERT: A 572 LYS cc_start: 0.8446 (tttt) cc_final: 0.8198 (tttt) REVERT: A 635 MET cc_start: 0.7623 (mmm) cc_final: 0.7250 (tmm) REVERT: A 680 PHE cc_start: 0.8407 (m-80) cc_final: 0.8185 (m-80) REVERT: A 693 MET cc_start: 0.7180 (mmp) cc_final: 0.6977 (mmm) REVERT: A 825 MET cc_start: 0.3568 (mtt) cc_final: 0.3144 (mtt) REVERT: B 109 ARG cc_start: 0.6886 (mpt180) cc_final: 0.6493 (mmt-90) REVERT: C 133 MET cc_start: 0.5065 (mmt) cc_final: 0.4541 (mmp) REVERT: C 243 MET cc_start: 0.8518 (mtp) cc_final: 0.7931 (mpp) REVERT: D 495 TYR cc_start: 0.7145 (OUTLIER) cc_final: 0.6762 (t80) REVERT: D 511 TYR cc_start: 0.6013 (OUTLIER) cc_final: 0.3966 (m-80) REVERT: D 542 MET cc_start: 0.8628 (mmp) cc_final: 0.7485 (ptt) REVERT: D 635 MET cc_start: 0.7992 (mmp) cc_final: 0.7689 (mmp) REVERT: D 680 PHE cc_start: 0.7946 (m-80) cc_final: 0.7535 (m-10) REVERT: F 134 PHE cc_start: 0.6290 (m-80) cc_final: 0.4663 (m-80) outliers start: 61 outliers final: 45 residues processed: 259 average time/residue: 0.7830 time to fit residues: 288.6696 Evaluate side-chains 226 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 176 time to evaluate : 2.868 ------------------------------------------------------------------------------- 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 153 ILE Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 328 TRP Chi-restraints excluded: chain A residue 354 ASN 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 A residue 677 MET Chi-restraints excluded: chain B residue 21 GLN Chi-restraints excluded: chain B residue 58 CYS Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 125 HIS Chi-restraints excluded: chain C residue 194 LEU 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 275 ASN Chi-restraints excluded: chain D residue 279 ARG Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 302 LEU Chi-restraints excluded: chain D residue 328 TRP Chi-restraints excluded: chain D residue 354 ASN Chi-restraints excluded: chain D residue 495 TYR Chi-restraints excluded: chain D residue 503 SER 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 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 E residue 125 HIS Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain F residue 233 HIS Chi-restraints excluded: chain F residue 239 ASN Chi-restraints excluded: chain F residue 289 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 67 optimal weight: 9.9990 chunk 126 optimal weight: 2.9990 chunk 201 optimal weight: 20.0000 chunk 125 optimal weight: 0.7980 chunk 115 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 116 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 168 optimal weight: 30.0000 chunk 94 optimal weight: 20.0000 chunk 104 optimal weight: 5.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- 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 ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 GLN ** C 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN E 114 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.164146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.130709 restraints weight = 144537.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.131921 restraints weight = 83878.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.133834 restraints weight = 66366.832| |-----------------------------------------------------------------------------| r_work (final): 0.4142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6704 moved from start: 0.8386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17104 Z= 0.133 Angle : 0.569 7.186 23112 Z= 0.299 Chirality : 0.039 0.152 2520 Planarity : 0.005 0.060 3002 Dihedral : 4.600 21.859 2284 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.13 % Allowed : 13.37 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.18), residues: 2034 helix: 0.49 (0.16), residues: 970 sheet: -1.05 (0.32), residues: 240 loop : -0.28 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 139 HIS 0.003 0.001 HIS A 632 PHE 0.016 0.002 PHE B 76 TYR 0.017 0.001 TYR B 99 ARG 0.016 0.001 ARG A 245 Details of bonding type rmsd hydrogen bonds : bond 0.04215 ( 844) hydrogen bonds : angle 5.23656 ( 2352) metal coordination : bond 0.00827 ( 24) metal coordination : angle 2.93738 ( 30) covalent geometry : bond 0.00295 (17080) covalent geometry : angle 0.55975 (23082) *********************** 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: 40 poor density : 200 time to evaluate : 2.413 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: A 495 TYR cc_start: 0.7205 (OUTLIER) cc_final: 0.6372 (t80) REVERT: A 573 GLU cc_start: 0.9019 (tt0) cc_final: 0.8019 (tp30) REVERT: A 635 MET cc_start: 0.7955 (mmm) cc_final: 0.7718 (tmm) REVERT: A 680 PHE cc_start: 0.8429 (m-80) cc_final: 0.8220 (m-80) REVERT: A 825 MET cc_start: 0.3212 (mtt) cc_final: 0.2898 (mtt) REVERT: B 83 TYR cc_start: 0.8044 (m-80) cc_final: 0.7793 (m-10) REVERT: B 109 ARG cc_start: 0.6844 (mpt180) cc_final: 0.6337 (mmt-90) REVERT: C 243 MET cc_start: 0.8597 (mtp) cc_final: 0.7960 (mpp) REVERT: D 476 SER cc_start: 0.8391 (t) cc_final: 0.7892 (m) REVERT: D 488 THR cc_start: 0.8093 (m) cc_final: 0.7851 (p) REVERT: D 495 TYR cc_start: 0.7000 (OUTLIER) cc_final: 0.6568 (t80) REVERT: D 511 TYR cc_start: 0.5497 (OUTLIER) cc_final: 0.3366 (m-80) REVERT: D 542 MET cc_start: 0.8645 (mmp) cc_final: 0.7230 (ptt) REVERT: D 680 PHE cc_start: 0.8073 (m-80) cc_final: 0.7672 (m-10) REVERT: E 83 TYR cc_start: 0.7892 (m-80) cc_final: 0.7660 (m-10) REVERT: F 133 MET cc_start: 0.5081 (mmm) cc_final: 0.4854 (mmm) outliers start: 40 outliers final: 30 residues processed: 231 average time/residue: 0.7693 time to fit residues: 252.8739 Evaluate side-chains 217 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 184 time to evaluate : 2.913 ------------------------------------------------------------------------------- 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 291 MET Chi-restraints excluded: chain A residue 296 LEU 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 648 PHE Chi-restraints excluded: chain A residue 723 ASN Chi-restraints excluded: chain B residue 125 HIS 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 279 ARG Chi-restraints excluded: chain D residue 328 TRP 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 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 239 ASN Chi-restraints excluded: chain F residue 246 MET Chi-restraints excluded: chain F residue 289 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 137 optimal weight: 3.9990 chunk 173 optimal weight: 4.9990 chunk 181 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 199 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 104 optimal weight: 5.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 167 GLN ** D 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 GLN ** 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 = 0.4629 r_free = 0.4629 target = 0.163504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.128755 restraints weight = 145179.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.130877 restraints weight = 92658.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.133019 restraints weight = 65722.806| |-----------------------------------------------------------------------------| r_work (final): 0.4149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6707 moved from start: 0.8604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17104 Z= 0.136 Angle : 0.544 7.172 23112 Z= 0.288 Chirality : 0.039 0.151 2520 Planarity : 0.005 0.072 3002 Dihedral : 4.345 21.091 2284 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.24 % Allowed : 14.00 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.18), residues: 2034 helix: 0.76 (0.16), residues: 984 sheet: -1.01 (0.32), residues: 240 loop : -0.09 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 139 HIS 0.004 0.001 HIS A 632 PHE 0.016 0.001 PHE A 482 TYR 0.013 0.001 TYR E 99 ARG 0.012 0.001 ARG D 506 Details of bonding type rmsd hydrogen bonds : bond 0.03956 ( 844) hydrogen bonds : angle 5.09280 ( 2352) metal coordination : bond 0.00750 ( 24) metal coordination : angle 2.42706 ( 30) covalent geometry : bond 0.00302 (17080) covalent geometry : angle 0.53755 (23082) *********************** 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 231 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 189 time to evaluate : 2.851 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: A 495 TYR cc_start: 0.7307 (OUTLIER) cc_final: 0.6493 (t80) REVERT: A 511 TYR cc_start: 0.4780 (OUTLIER) cc_final: 0.2885 (m-80) REVERT: A 573 GLU cc_start: 0.9075 (tt0) cc_final: 0.8060 (tp30) REVERT: A 825 MET cc_start: 0.3069 (mtt) cc_final: 0.2769 (mtt) REVERT: B 83 TYR cc_start: 0.8098 (m-80) cc_final: 0.7815 (m-10) REVERT: B 109 ARG cc_start: 0.6837 (mpt180) cc_final: 0.6069 (mmt90) REVERT: C 243 MET cc_start: 0.8631 (mtp) cc_final: 0.8040 (mpp) REVERT: D 476 SER cc_start: 0.8671 (t) cc_final: 0.8357 (m) REVERT: D 488 THR cc_start: 0.8033 (m) cc_final: 0.7599 (p) REVERT: D 490 ASN cc_start: 0.8122 (t0) cc_final: 0.7849 (t0) REVERT: D 495 TYR cc_start: 0.7025 (OUTLIER) cc_final: 0.6621 (t80) REVERT: D 511 TYR cc_start: 0.5365 (OUTLIER) cc_final: 0.3185 (m-80) REVERT: D 542 MET cc_start: 0.8732 (mmp) cc_final: 0.7379 (ptt) REVERT: D 618 VAL cc_start: 0.8296 (t) cc_final: 0.7781 (p) REVERT: D 680 PHE cc_start: 0.8093 (m-80) cc_final: 0.7693 (m-10) REVERT: D 825 MET cc_start: 0.3337 (mtt) cc_final: 0.2874 (mtt) REVERT: E 46 ARG cc_start: 0.7459 (tpp-160) cc_final: 0.7168 (tpp-160) REVERT: E 83 TYR cc_start: 0.7979 (m-80) cc_final: 0.7645 (m-10) REVERT: F 133 MET cc_start: 0.5180 (mmm) cc_final: 0.4902 (mmm) outliers start: 42 outliers final: 34 residues processed: 221 average time/residue: 0.7965 time to fit residues: 251.8753 Evaluate side-chains 221 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 183 time to evaluate : 2.650 ------------------------------------------------------------------------------- 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 291 MET Chi-restraints excluded: chain A residue 296 LEU 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 648 PHE Chi-restraints excluded: chain A residue 723 ASN 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 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 328 TRP Chi-restraints excluded: chain D residue 495 TYR Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain D residue 511 TYR Chi-restraints excluded: chain D residue 522 TYR 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 E residue 140 THR Chi-restraints excluded: chain F residue 239 ASN Chi-restraints excluded: chain F residue 246 MET Chi-restraints excluded: chain F residue 289 LEU 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 58 optimal weight: 40.0000 chunk 201 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 203 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 188 optimal weight: 0.8980 chunk 146 optimal weight: 0.6980 chunk 159 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 GLN ** 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 = 0.4633 r_free = 0.4633 target = 0.163896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.129890 restraints weight = 143191.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.131876 restraints weight = 91511.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.133982 restraints weight = 63967.518| |-----------------------------------------------------------------------------| r_work (final): 0.4158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6706 moved from start: 0.8805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17104 Z= 0.131 Angle : 0.529 6.395 23112 Z= 0.278 Chirality : 0.038 0.149 2520 Planarity : 0.004 0.057 3002 Dihedral : 4.208 20.489 2284 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.18 % Allowed : 14.16 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.19), residues: 2034 helix: 0.99 (0.16), residues: 984 sheet: -0.89 (0.32), residues: 240 loop : -0.00 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 139 HIS 0.003 0.001 HIS B 85 PHE 0.015 0.001 PHE E 76 TYR 0.013 0.001 TYR A 502 ARG 0.007 0.000 ARG A 245 Details of bonding type rmsd hydrogen bonds : bond 0.03782 ( 844) hydrogen bonds : angle 4.98122 ( 2352) metal coordination : bond 0.00588 ( 24) metal coordination : angle 2.18558 ( 30) covalent geometry : bond 0.00293 (17080) covalent geometry : angle 0.52379 (23082) *********************** 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 233 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 192 time to evaluate : 2.509 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: A 495 TYR cc_start: 0.7190 (OUTLIER) cc_final: 0.6437 (t80) REVERT: A 511 TYR cc_start: 0.5282 (OUTLIER) cc_final: 0.2612 (m-80) REVERT: A 825 MET cc_start: 0.3300 (mtt) cc_final: 0.3054 (mtt) REVERT: B 83 TYR cc_start: 0.8040 (m-80) cc_final: 0.7750 (m-10) REVERT: B 109 ARG cc_start: 0.6845 (mpt180) cc_final: 0.5982 (mmt90) REVERT: C 243 MET cc_start: 0.8692 (mtp) cc_final: 0.8015 (mpp) REVERT: D 476 SER cc_start: 0.8552 (t) cc_final: 0.8235 (m) REVERT: D 488 THR cc_start: 0.7714 (m) cc_final: 0.7390 (p) REVERT: D 490 ASN cc_start: 0.8042 (t0) cc_final: 0.7789 (t0) REVERT: D 495 TYR cc_start: 0.6880 (OUTLIER) cc_final: 0.6549 (t80) REVERT: D 511 TYR cc_start: 0.5535 (OUTLIER) cc_final: 0.3422 (m-80) REVERT: D 680 PHE cc_start: 0.8102 (m-80) cc_final: 0.7673 (m-10) REVERT: D 825 MET cc_start: 0.3421 (mtt) cc_final: 0.2927 (mtt) REVERT: E 83 TYR cc_start: 0.7908 (m-80) cc_final: 0.7624 (m-10) outliers start: 41 outliers final: 33 residues processed: 221 average time/residue: 0.7713 time to fit residues: 244.6902 Evaluate side-chains 220 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 183 time to evaluate : 2.381 ------------------------------------------------------------------------------- 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 291 MET Chi-restraints excluded: chain A residue 296 LEU 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 648 PHE Chi-restraints excluded: chain A residue 723 ASN 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 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 328 TRP 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 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 E residue 140 THR Chi-restraints excluded: chain F residue 239 ASN Chi-restraints excluded: chain F residue 246 MET Chi-restraints excluded: chain F residue 289 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 54 optimal weight: 2.9990 chunk 158 optimal weight: 0.0170 chunk 203 optimal weight: 4.9990 chunk 173 optimal weight: 6.9990 chunk 124 optimal weight: 0.9980 chunk 138 optimal weight: 0.0470 chunk 129 optimal weight: 1.9990 chunk 196 optimal weight: 20.0000 chunk 49 optimal weight: 8.9990 chunk 31 optimal weight: 0.6980 chunk 149 optimal weight: 0.6980 overall best weight: 0.4916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 GLN ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 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 = 0.4659 r_free = 0.4659 target = 0.169274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.137420 restraints weight = 141043.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.139221 restraints weight = 83491.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.140194 restraints weight = 59270.241| |-----------------------------------------------------------------------------| r_work (final): 0.4199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6586 moved from start: 0.8830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 17104 Z= 0.100 Angle : 0.516 8.340 23112 Z= 0.266 Chirality : 0.038 0.172 2520 Planarity : 0.004 0.055 3002 Dihedral : 3.926 18.593 2284 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.65 % Allowed : 14.96 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.19), residues: 2034 helix: 1.36 (0.17), residues: 984 sheet: -0.73 (0.33), residues: 240 loop : 0.21 (0.23), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 139 HIS 0.004 0.000 HIS F 179 PHE 0.015 0.001 PHE A 482 TYR 0.012 0.001 TYR A 502 ARG 0.008 0.000 ARG A 245 Details of bonding type rmsd hydrogen bonds : bond 0.03351 ( 844) hydrogen bonds : angle 4.72344 ( 2352) metal coordination : bond 0.00685 ( 24) metal coordination : angle 2.08830 ( 30) covalent geometry : bond 0.00226 (17080) covalent geometry : angle 0.51072 (23082) *********************** 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 236 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 205 time to evaluate : 2.512 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: A 151 ARG cc_start: 0.7802 (OUTLIER) cc_final: 0.7585 (ttp80) REVERT: A 495 TYR cc_start: 0.7176 (OUTLIER) cc_final: 0.6378 (t80) REVERT: A 511 TYR cc_start: 0.5282 (OUTLIER) cc_final: 0.2750 (m-80) REVERT: A 825 MET cc_start: 0.3124 (mtt) cc_final: 0.2882 (mtt) REVERT: B 83 TYR cc_start: 0.8009 (m-80) cc_final: 0.7681 (m-10) REVERT: B 109 ARG cc_start: 0.6681 (mpt180) cc_final: 0.6047 (mmt90) REVERT: C 243 MET cc_start: 0.8739 (mtp) cc_final: 0.8004 (mpp) REVERT: D 339 MET cc_start: 0.7782 (mtm) cc_final: 0.7409 (mtt) REVERT: D 488 THR cc_start: 0.7798 (m) cc_final: 0.7439 (p) REVERT: D 495 TYR cc_start: 0.7074 (OUTLIER) cc_final: 0.6679 (t80) REVERT: D 511 TYR cc_start: 0.5631 (OUTLIER) cc_final: 0.4034 (m-80) REVERT: D 542 MET cc_start: 0.8816 (mmp) cc_final: 0.7543 (ptt) REVERT: D 618 VAL cc_start: 0.8314 (t) cc_final: 0.7835 (p) REVERT: D 680 PHE cc_start: 0.8074 (m-80) cc_final: 0.7649 (m-10) REVERT: E 83 TYR cc_start: 0.7878 (m-80) cc_final: 0.7623 (m-10) REVERT: F 120 LYS cc_start: 0.4725 (tttt) cc_final: 0.4378 (mtmt) outliers start: 31 outliers final: 25 residues processed: 228 average time/residue: 0.7880 time to fit residues: 258.2654 Evaluate side-chains 228 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 198 time to evaluate : 2.720 ------------------------------------------------------------------------------- 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 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 511 TYR Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 648 PHE Chi-restraints excluded: chain A residue 723 ASN Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 125 HIS Chi-restraints excluded: chain C residue 286 GLU 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 328 TRP 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 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 71 ASP Chi-restraints excluded: chain F residue 239 ASN Chi-restraints excluded: chain F residue 246 MET Chi-restraints excluded: chain F residue 289 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 36 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 chunk 58 optimal weight: 8.9990 chunk 183 optimal weight: 6.9990 chunk 125 optimal weight: 0.9980 chunk 53 optimal weight: 8.9990 chunk 198 optimal weight: 8.9990 chunk 85 optimal weight: 4.9990 chunk 159 optimal weight: 10.0000 chunk 10 optimal weight: 0.6980 chunk 134 optimal weight: 9.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 GLN ** 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 = 0.4612 r_free = 0.4612 target = 0.162105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.127128 restraints weight = 144543.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.129711 restraints weight = 92981.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.131272 restraints weight = 67340.807| |-----------------------------------------------------------------------------| r_work (final): 0.4102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6798 moved from start: 0.9207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17104 Z= 0.183 Angle : 0.578 7.047 23112 Z= 0.308 Chirality : 0.039 0.155 2520 Planarity : 0.005 0.056 3002 Dihedral : 4.225 20.809 2284 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.60 % Allowed : 15.12 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.18), residues: 2034 helix: 1.00 (0.16), residues: 982 sheet: -0.88 (0.32), residues: 240 loop : -0.06 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 791 HIS 0.005 0.001 HIS A 632 PHE 0.015 0.002 PHE E 54 TYR 0.020 0.002 TYR A 243 ARG 0.006 0.001 ARG B 17 Details of bonding type rmsd hydrogen bonds : bond 0.04105 ( 844) hydrogen bonds : angle 5.11561 ( 2352) metal coordination : bond 0.00949 ( 24) metal coordination : angle 2.37920 ( 30) covalent geometry : bond 0.00401 (17080) covalent geometry : angle 0.57150 (23082) ********************** 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 223 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 193 time to evaluate : 2.508 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: A 135 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7177 (mm-30) REVERT: A 495 TYR cc_start: 0.6884 (OUTLIER) cc_final: 0.6422 (t80) REVERT: A 511 TYR cc_start: 0.5180 (OUTLIER) cc_final: 0.2707 (m-80) REVERT: A 825 MET cc_start: 0.3193 (mtt) cc_final: 0.2952 (mtt) REVERT: B 48 GLU cc_start: 0.8866 (mt-10) cc_final: 0.8179 (tp30) REVERT: B 109 ARG cc_start: 0.6790 (mpt180) cc_final: 0.6414 (mmt90) REVERT: C 243 MET cc_start: 0.8713 (mtp) cc_final: 0.7911 (mpp) REVERT: D 476 SER cc_start: 0.8590 (t) cc_final: 0.8287 (m) REVERT: D 495 TYR cc_start: 0.7158 (OUTLIER) cc_final: 0.6752 (t80) REVERT: D 511 TYR cc_start: 0.5587 (OUTLIER) cc_final: 0.3798 (m-80) REVERT: D 572 LYS cc_start: 0.7630 (tttt) cc_final: 0.7388 (mmtt) REVERT: D 618 VAL cc_start: 0.8387 (t) cc_final: 0.8111 (p) REVERT: D 680 PHE cc_start: 0.8001 (m-80) cc_final: 0.7561 (m-10) REVERT: D 712 GLU cc_start: 0.8282 (tt0) cc_final: 0.7968 (mp0) REVERT: E 83 TYR cc_start: 0.8052 (m-80) cc_final: 0.7757 (m-10) outliers start: 30 outliers final: 25 residues processed: 214 average time/residue: 0.7916 time to fit residues: 243.7725 Evaluate side-chains 213 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 184 time to evaluate : 2.806 ------------------------------------------------------------------------------- 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 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 648 PHE Chi-restraints excluded: chain A residue 723 ASN Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 125 HIS Chi-restraints excluded: chain C residue 286 GLU 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 328 TRP 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 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 71 ASP Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain F residue 239 ASN Chi-restraints excluded: chain F residue 289 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 40 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 97 optimal weight: 10.0000 chunk 120 optimal weight: 2.9990 chunk 127 optimal weight: 0.9990 chunk 168 optimal weight: 20.0000 chunk 29 optimal weight: 0.5980 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 GLN ** 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 = 0.4618 r_free = 0.4618 target = 0.162655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.130039 restraints weight = 142706.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.131949 restraints weight = 89660.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.132888 restraints weight = 61427.775| |-----------------------------------------------------------------------------| r_work (final): 0.4140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6702 moved from start: 0.9343 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= 0.126 Angle : 0.533 7.708 23112 Z= 0.278 Chirality : 0.038 0.149 2520 Planarity : 0.004 0.056 3002 Dihedral : 4.070 19.973 2284 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.60 % Allowed : 15.23 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.19), residues: 2034 helix: 1.17 (0.17), residues: 984 sheet: -0.79 (0.33), residues: 234 loop : 0.02 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 139 HIS 0.004 0.001 HIS E 85 PHE 0.014 0.001 PHE A 482 TYR 0.012 0.001 TYR A 502 ARG 0.006 0.000 ARG B 17 Details of bonding type rmsd hydrogen bonds : bond 0.03660 ( 844) hydrogen bonds : angle 4.90700 ( 2352) metal coordination : bond 0.00620 ( 24) metal coordination : angle 2.19207 ( 30) covalent geometry : bond 0.00285 (17080) covalent geometry : angle 0.52696 (23082) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10223.85 seconds wall clock time: 175 minutes 49.83 seconds (10549.83 seconds total)