Starting phenix.real_space_refine on Fri Mar 22 11:02:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r1g_18810/03_2024/8r1g_18810.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r1g_18810/03_2024/8r1g_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r1g_18810/03_2024/8r1g_18810.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r1g_18810/03_2024/8r1g_18810.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r1g_18810/03_2024/8r1g_18810.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r1g_18810/03_2024/8r1g_18810.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 33258 Number of models: 1 Model: "" Number of chains: 10 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: "D" 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: "E" 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: "F" 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} Chain: "E" 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: "F" 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 ATOM 29461 SG CYS E 110 83.900 48.590 46.629 1.00 65.99 S ATOM 29504 SG CYS E 113 83.446 47.869 43.256 1.00 66.82 S ATOM 30031 SG CYS E 143 81.389 50.778 44.815 1.00 67.41 S ATOM 30055 SG CYS E 146 80.447 47.254 45.593 1.00 72.71 S ATOM 28231 SG CYS E 37 91.546 36.803 37.014 1.00 91.45 S ATOM 28278 SG CYS E 40 90.120 33.544 36.293 1.00 85.52 S ATOM 28784 SG CYS E 70 87.883 36.780 36.885 1.00 82.71 S ATOM 28828 SG CYS E 73 89.563 35.084 39.738 1.00 79.69 S ATOM 31440 SG CYS F 176 91.324 80.561 20.019 1.00183.48 S ATOM 32403 SG CYS F 238 92.967 78.302 22.892 1.00173.40 S ATOM 32449 SG CYS F 242 89.328 77.912 21.982 1.00170.91 S Time building chain proxies: 14.49, per 1000 atoms: 0.44 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 - 3.50 Amino acid : False - 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: 28.77 Conformation dependent library (CDL) restraints added in 3.2 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: 2.95 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: 13.38 Time building geometry restraints manager: 29.74 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: 99.26 - 106.21: 697 106.21 - 113.17: 38636 113.17 - 120.12: 10980 120.12 - 127.08: 10225 127.08 - 134.03: 150 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 1.850 nonbonded pdb=" OH TYR A 262 " pdb=" HZ1 LYS D 311 " model vdw 1.543 1.850 nonbonded pdb=" OH TYR A 262 " pdb=" NZ LYS D 311 " model vdw 1.603 2.350 nonbonded pdb=" OE2 GLU A 130 " pdb=" HH TYR A 134 " model vdw 1.680 1.850 nonbonded pdb=" OE2 GLU D 130 " pdb=" HH TYR D 134 " model vdw 1.681 1.850 ... (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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.460 Extract box with map and model: 3.130 Check model and map are aligned: 0.450 Set scattering table: 0.320 Process input model: 113.190 Find NCS groups from input model: 1.280 Set up NCS constraints: 0.170 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.430 ------------------------------------------------------------------------------- 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 17080 Z= 0.397 Angle : 0.921 8.676 23082 Z= 0.533 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 *********************** 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 fitting. rotamer outliers: 5 poor density : 468 time to evaluate : 2.765 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: 0.8084 time to fit residues: 528.5284 Evaluate side-chains 272 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 271 time to evaluate : 2.637 ------------------------------------------------------------------------------- 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: 6.9990 chunk 52 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 82 optimal weight: 8.9990 chunk 159 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 97 optimal weight: 9.9990 chunk 119 optimal weight: 3.9990 chunk 185 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 165 GLN F 167 GLN F 288 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6220 moved from start: 0.4694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 17080 Z= 0.384 Angle : 0.724 6.295 23082 Z= 0.403 Chirality : 0.042 0.206 2520 Planarity : 0.006 0.046 3002 Dihedral : 4.896 41.311 2285 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.24 % Allowed : 9.64 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.11 (0.18), residues: 2034 helix: 0.18 (0.16), residues: 980 sheet: -0.41 (0.35), residues: 214 loop : -0.07 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 791 HIS 0.009 0.002 HIS B 85 PHE 0.030 0.002 PHE B 52 TYR 0.025 0.003 TYR E 67 ARG 0.008 0.001 ARG B 46 *********************** 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 308 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 266 time to evaluate : 2.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 495 TYR cc_start: 0.7394 (OUTLIER) cc_final: 0.6356 (t80) REVERT: A 545 MET cc_start: 0.6790 (tpp) cc_final: 0.6428 (tpp) REVERT: A 550 ASP cc_start: 0.7065 (m-30) cc_final: 0.6576 (t70) REVERT: A 680 PHE cc_start: 0.8475 (m-80) cc_final: 0.8183 (m-80) REVERT: A 693 MET cc_start: 0.6085 (mmp) cc_final: 0.5727 (mmm) REVERT: A 739 MET cc_start: 0.7762 (mtt) cc_final: 0.7226 (ttm) REVERT: A 825 MET cc_start: 0.2914 (mtt) cc_final: 0.2498 (mtt) REVERT: B 79 LYS cc_start: 0.7678 (tptt) cc_final: 0.7054 (ttmt) REVERT: C 243 MET cc_start: 0.8387 (mtp) cc_final: 0.7827 (mpp) REVERT: D 291 MET cc_start: 0.7836 (mmm) cc_final: 0.7500 (tpp) REVERT: D 313 MET cc_start: 0.8616 (ttm) cc_final: 0.8341 (ttm) REVERT: D 339 MET cc_start: 0.7506 (mtm) cc_final: 0.7258 (mtt) REVERT: D 366 ASP cc_start: 0.8176 (OUTLIER) cc_final: 0.7747 (t70) REVERT: D 460 MET cc_start: 0.7614 (mmm) cc_final: 0.7013 (mmm) REVERT: D 488 THR cc_start: 0.8784 (m) cc_final: 0.8351 (p) REVERT: D 495 TYR cc_start: 0.7229 (OUTLIER) cc_final: 0.6449 (t80) REVERT: D 550 ASP cc_start: 0.7152 (m-30) cc_final: 0.6788 (t70) REVERT: D 572 LYS cc_start: 0.8832 (tttt) cc_final: 0.8534 (tttt) REVERT: D 680 PHE cc_start: 0.8108 (m-80) cc_final: 0.7676 (m-80) REVERT: D 825 MET cc_start: 0.3258 (mtt) cc_final: 0.2978 (mtt) REVERT: E 109 ARG cc_start: 0.6853 (mtt-85) cc_final: 0.6503 (mmt90) REVERT: F 282 ARG cc_start: 0.6241 (ttt180) cc_final: 0.6026 (ttt180) outliers start: 42 outliers final: 28 residues processed: 297 average time/residue: 0.7112 time to fit residues: 306.1333 Evaluate side-chains 246 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 215 time to evaluate : 2.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 426 ASP 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 290 VAL Chi-restraints excluded: chain D residue 366 ASP Chi-restraints excluded: chain D residue 471 THR 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 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 102 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 154 optimal weight: 9.9990 chunk 126 optimal weight: 3.9990 chunk 51 optimal weight: 9.9990 chunk 185 optimal weight: 10.0000 chunk 200 optimal weight: 10.0000 chunk 165 optimal weight: 20.0000 chunk 184 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 148 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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 393 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 554 GLN ** E 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN E 114 GLN F 100 GLN F 104 GLN ** F 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6733 moved from start: 0.7759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.088 17080 Z= 0.651 Angle : 0.976 9.837 23082 Z= 0.555 Chirality : 0.050 0.214 2520 Planarity : 0.009 0.114 3002 Dihedral : 6.481 58.708 2285 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 30.62 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.18 % Favored : 92.63 % Rotamer: Outliers : 4.37 % Allowed : 12.89 % Favored : 82.75 % 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: -1.90 (0.17), residues: 2034 helix: -1.20 (0.15), residues: 998 sheet: -1.28 (0.34), residues: 212 loop : -1.09 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP C 146 HIS 0.017 0.003 HIS B 85 PHE 0.035 0.005 PHE D 590 TYR 0.032 0.004 TYR B 99 ARG 0.018 0.001 ARG F 156 *********************** 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 307 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 225 time to evaluate : 2.609 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: A 242 VAL cc_start: 0.8164 (t) cc_final: 0.7947 (t) REVERT: A 339 MET cc_start: 0.7947 (mtt) cc_final: 0.7652 (mtt) REVERT: A 495 TYR cc_start: 0.7561 (OUTLIER) cc_final: 0.6719 (t80) REVERT: A 511 TYR cc_start: 0.4935 (OUTLIER) cc_final: 0.2952 (m-80) REVERT: A 572 LYS cc_start: 0.8708 (tttt) cc_final: 0.8476 (tttt) REVERT: A 635 MET cc_start: 0.7839 (mmm) cc_final: 0.7483 (ttm) REVERT: A 680 PHE cc_start: 0.8876 (m-80) cc_final: 0.8650 (m-10) REVERT: A 693 MET cc_start: 0.7175 (mmp) cc_final: 0.6908 (mmm) REVERT: A 825 MET cc_start: 0.3701 (mtt) cc_final: 0.3279 (mtt) REVERT: C 243 MET cc_start: 0.8696 (mtp) cc_final: 0.7854 (mpp) REVERT: D 340 MET cc_start: 0.8881 (tmm) cc_final: 0.8580 (tmm) REVERT: D 349 TYR cc_start: 0.7656 (OUTLIER) cc_final: 0.7358 (t80) REVERT: D 366 ASP cc_start: 0.8384 (OUTLIER) cc_final: 0.7904 (t0) REVERT: D 394 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7707 (mm-30) REVERT: D 395 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.5760 (tp30) REVERT: D 495 TYR cc_start: 0.7307 (OUTLIER) cc_final: 0.6790 (t80) REVERT: D 510 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8971 (tt) REVERT: D 511 TYR cc_start: 0.5313 (OUTLIER) cc_final: 0.3497 (m-80) REVERT: D 525 LEU cc_start: 0.5502 (mt) cc_final: 0.5238 (mt) REVERT: D 545 MET cc_start: 0.8256 (tpp) cc_final: 0.7891 (tpp) REVERT: D 680 PHE cc_start: 0.8485 (m-80) cc_final: 0.8090 (m-10) outliers start: 82 outliers final: 50 residues processed: 287 average time/residue: 0.7779 time to fit residues: 318.1751 Evaluate side-chains 240 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 181 time to evaluate : 2.847 ------------------------------------------------------------------------------- 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 325 ILE Chi-restraints excluded: chain A residue 354 ASN Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 490 ASN Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 501 MET 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 642 MET Chi-restraints excluded: chain A residue 653 ASP Chi-restraints excluded: chain A residue 723 ASN Chi-restraints excluded: chain A residue 753 GLU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 110 CYS 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 253 GLU Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 293 ASN Chi-restraints excluded: chain D residue 328 TRP Chi-restraints excluded: chain D residue 349 TYR Chi-restraints excluded: chain D residue 354 ASN Chi-restraints excluded: chain D residue 366 ASP Chi-restraints excluded: chain D residue 394 GLU Chi-restraints excluded: chain D residue 395 GLU Chi-restraints excluded: chain D residue 495 TYR Chi-restraints excluded: chain D residue 501 MET Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 511 TYR Chi-restraints excluded: chain D residue 522 TYR Chi-restraints excluded: chain D residue 635 MET Chi-restraints excluded: chain D residue 653 ASP Chi-restraints excluded: chain D residue 713 PHE Chi-restraints excluded: chain D residue 723 ASN 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 100 GLN 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 183 optimal weight: 0.6980 chunk 139 optimal weight: 9.9990 chunk 96 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 124 optimal weight: 0.5980 chunk 186 optimal weight: 7.9990 chunk 197 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 176 optimal weight: 0.8980 chunk 53 optimal weight: 6.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 ** E 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 HIS E 98 GLN ** F 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6561 moved from start: 0.7926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 17080 Z= 0.212 Angle : 0.597 6.901 23082 Z= 0.321 Chirality : 0.039 0.154 2520 Planarity : 0.005 0.050 3002 Dihedral : 5.152 57.281 2285 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.04 % Allowed : 14.38 % Favored : 82.59 % 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: -0.62 (0.18), residues: 2034 helix: -0.01 (0.16), residues: 984 sheet: -1.07 (0.35), residues: 216 loop : -0.54 (0.22), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 139 HIS 0.004 0.001 HIS A 632 PHE 0.019 0.002 PHE C 134 TYR 0.016 0.001 TYR F 234 ARG 0.009 0.001 ARG C 283 *********************** 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 265 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 208 time to evaluate : 2.994 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: A 495 TYR cc_start: 0.6817 (OUTLIER) cc_final: 0.6346 (t80) REVERT: A 572 LYS cc_start: 0.8787 (tttt) cc_final: 0.8115 (tptt) REVERT: A 635 MET cc_start: 0.8035 (mmm) cc_final: 0.7652 (ttm) REVERT: A 680 PHE cc_start: 0.8914 (m-80) cc_final: 0.8665 (m-10) REVERT: A 693 MET cc_start: 0.6942 (mmp) cc_final: 0.6681 (mmm) REVERT: A 711 LYS cc_start: 0.7736 (tptt) cc_final: 0.7512 (tppt) REVERT: A 825 MET cc_start: 0.3427 (mtt) cc_final: 0.2878 (mtt) REVERT: B 109 ARG cc_start: 0.6826 (mpt180) cc_final: 0.6296 (mmt-90) REVERT: C 169 MET cc_start: 0.6637 (ttt) cc_final: 0.6085 (ttm) REVERT: C 243 MET cc_start: 0.8474 (mtp) cc_final: 0.7703 (mpp) REVERT: D 495 TYR cc_start: 0.7064 (OUTLIER) cc_final: 0.6637 (t80) REVERT: D 511 TYR cc_start: 0.5685 (OUTLIER) cc_final: 0.3183 (m-80) REVERT: D 525 LEU cc_start: 0.6278 (mt) cc_final: 0.6017 (mt) REVERT: D 542 MET cc_start: 0.8463 (mmp) cc_final: 0.7262 (ptt) REVERT: D 545 MET cc_start: 0.8246 (tpp) cc_final: 0.7953 (tpp) REVERT: D 550 ASP cc_start: 0.6959 (m-30) cc_final: 0.6457 (t70) REVERT: D 680 PHE cc_start: 0.8405 (m-80) cc_final: 0.7987 (m-80) REVERT: D 825 MET cc_start: 0.3214 (mtt) cc_final: 0.2779 (mtt) REVERT: E 48 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8272 (tp30) REVERT: E 109 ARG cc_start: 0.7183 (mtt-85) cc_final: 0.6425 (mmt180) outliers start: 57 outliers final: 39 residues processed: 248 average time/residue: 0.7998 time to fit residues: 281.3703 Evaluate side-chains 226 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 184 time to evaluate : 2.635 ------------------------------------------------------------------------------- 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 236 ILE Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 426 ASP 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 110 CYS 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 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 302 LEU Chi-restraints excluded: chain D residue 328 TRP Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain D residue 483 ILE Chi-restraints excluded: chain D residue 495 TYR Chi-restraints excluded: chain D residue 503 SER 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 E residue 44 LEU 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 194 LEU Chi-restraints excluded: chain F residue 246 MET Chi-restraints excluded: chain F residue 263 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 164 optimal weight: 20.0000 chunk 111 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 168 optimal weight: 30.0000 chunk 136 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 100 optimal weight: 7.9990 chunk 176 optimal weight: 0.9990 chunk 49 optimal weight: 20.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 626 ASN ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 GLN ** F 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6662 moved from start: 0.8592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 17080 Z= 0.305 Angle : 0.624 7.203 23082 Z= 0.342 Chirality : 0.040 0.158 2520 Planarity : 0.005 0.049 3002 Dihedral : 5.014 52.284 2285 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 3.19 % Allowed : 14.96 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.67 (0.18), residues: 2034 helix: 0.01 (0.16), residues: 986 sheet: -1.19 (0.35), residues: 210 loop : -0.60 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 139 HIS 0.006 0.001 HIS C 115 PHE 0.020 0.002 PHE C 134 TYR 0.015 0.002 TYR A 511 ARG 0.008 0.001 ARG E 62 *********************** 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 252 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 192 time to evaluate : 2.673 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: A 495 TYR cc_start: 0.7089 (OUTLIER) cc_final: 0.6612 (t80) REVERT: A 511 TYR cc_start: 0.5186 (OUTLIER) cc_final: 0.2992 (m-80) REVERT: A 573 GLU cc_start: 0.9048 (tt0) cc_final: 0.8004 (tp30) REVERT: A 577 LEU cc_start: 0.8569 (mm) cc_final: 0.8345 (mm) REVERT: A 635 MET cc_start: 0.7515 (mmm) cc_final: 0.7076 (ttm) REVERT: A 680 PHE cc_start: 0.8793 (m-80) cc_final: 0.8534 (m-10) REVERT: A 711 LYS cc_start: 0.7949 (tptt) cc_final: 0.7357 (tppt) REVERT: A 825 MET cc_start: 0.3421 (mtt) cc_final: 0.2866 (mtt) REVERT: B 83 TYR cc_start: 0.8048 (m-80) cc_final: 0.7689 (m-10) REVERT: B 109 ARG cc_start: 0.6994 (mpt180) cc_final: 0.6419 (mmt-90) REVERT: C 169 MET cc_start: 0.7191 (ttt) cc_final: 0.6629 (ttt) REVERT: C 243 MET cc_start: 0.8556 (mtp) cc_final: 0.7727 (mpp) REVERT: D 339 MET cc_start: 0.7718 (mtt) cc_final: 0.7322 (mtt) REVERT: D 440 ARG cc_start: 0.3746 (tpm170) cc_final: 0.2988 (tpt170) REVERT: D 476 SER cc_start: 0.8705 (t) cc_final: 0.8332 (p) REVERT: D 495 TYR cc_start: 0.7105 (OUTLIER) cc_final: 0.6669 (t80) REVERT: D 511 TYR cc_start: 0.5640 (OUTLIER) cc_final: 0.3420 (m-80) REVERT: D 545 MET cc_start: 0.8296 (tpp) cc_final: 0.7964 (tpp) REVERT: D 573 GLU cc_start: 0.8874 (tt0) cc_final: 0.7762 (tp30) REVERT: D 577 LEU cc_start: 0.8824 (mt) cc_final: 0.8424 (mm) REVERT: D 680 PHE cc_start: 0.8364 (m-80) cc_final: 0.8138 (m-80) REVERT: D 825 MET cc_start: 0.3313 (mtt) cc_final: 0.2811 (mtt) REVERT: E 25 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.7157 (mm-30) REVERT: E 48 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8230 (tp30) REVERT: E 109 ARG cc_start: 0.7201 (mtt-85) cc_final: 0.6539 (mpt180) outliers start: 60 outliers final: 47 residues processed: 234 average time/residue: 0.7766 time to fit residues: 260.6705 Evaluate side-chains 233 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 181 time to evaluate : 2.803 ------------------------------------------------------------------------------- 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 291 MET Chi-restraints excluded: chain A residue 328 TRP Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 447 GLU 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 723 ASN Chi-restraints excluded: chain A residue 813 ASP Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 110 CYS 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 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 302 LEU Chi-restraints excluded: chain D residue 328 TRP Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain D residue 483 ILE Chi-restraints excluded: chain D residue 495 TYR Chi-restraints excluded: chain D residue 503 SER 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 589 MET 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 723 ASN Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 44 LEU 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 246 MET Chi-restraints excluded: chain F residue 263 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 66 optimal weight: 20.0000 chunk 177 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 chunk 48 optimal weight: 0.4980 chunk 197 optimal weight: 0.7980 chunk 163 optimal weight: 9.9990 chunk 91 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 HIS B 21 GLN C 131 ASN ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6607 moved from start: 0.8726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 17080 Z= 0.197 Angle : 0.543 5.999 23082 Z= 0.291 Chirality : 0.039 0.150 2520 Planarity : 0.004 0.049 3002 Dihedral : 4.658 53.910 2285 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.88 % Allowed : 15.12 % Favored : 82.00 % 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: 0.45 (0.16), residues: 984 sheet: -1.02 (0.37), residues: 210 loop : -0.44 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 139 HIS 0.002 0.001 HIS A 632 PHE 0.016 0.001 PHE A 482 TYR 0.013 0.001 TYR B 50 ARG 0.004 0.000 ARG E 46 *********************** 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 250 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 196 time to evaluate : 2.690 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: 0.6825 (OUTLIER) cc_final: 0.6441 (t80) REVERT: A 511 TYR cc_start: 0.5076 (OUTLIER) cc_final: 0.3089 (m-80) REVERT: A 573 GLU cc_start: 0.8990 (tt0) cc_final: 0.7994 (tp30) REVERT: A 577 LEU cc_start: 0.8515 (mm) cc_final: 0.8257 (mm) REVERT: A 635 MET cc_start: 0.7402 (mmm) cc_final: 0.7136 (ttm) REVERT: A 680 PHE cc_start: 0.8780 (m-80) cc_final: 0.8558 (m-10) REVERT: A 693 MET cc_start: 0.6626 (mmm) cc_final: 0.6336 (mmm) REVERT: A 825 MET cc_start: 0.3365 (mtt) cc_final: 0.2806 (mtt) REVERT: B 83 TYR cc_start: 0.8002 (m-80) cc_final: 0.7787 (m-10) REVERT: B 109 ARG cc_start: 0.6941 (mpt180) cc_final: 0.6402 (mmt-90) REVERT: C 169 MET cc_start: 0.7247 (ttt) cc_final: 0.6787 (ttt) REVERT: C 243 MET cc_start: 0.8571 (mtp) cc_final: 0.7702 (mpp) REVERT: D 339 MET cc_start: 0.7634 (mtt) cc_final: 0.7213 (mtt) REVERT: D 366 ASP cc_start: 0.7748 (m-30) cc_final: 0.7189 (t0) REVERT: D 374 CYS cc_start: 0.8316 (m) cc_final: 0.6972 (m) REVERT: D 440 ARG cc_start: 0.3626 (tpm170) cc_final: 0.3058 (tpt170) REVERT: D 476 SER cc_start: 0.8630 (t) cc_final: 0.8236 (p) REVERT: D 488 THR cc_start: 0.8132 (m) cc_final: 0.7837 (p) REVERT: D 495 TYR cc_start: 0.6969 (OUTLIER) cc_final: 0.6561 (t80) REVERT: D 511 TYR cc_start: 0.5533 (OUTLIER) cc_final: 0.3204 (m-80) REVERT: D 545 MET cc_start: 0.8205 (tpp) cc_final: 0.7863 (tpp) REVERT: D 680 PHE cc_start: 0.8378 (m-80) cc_final: 0.8135 (m-10) REVERT: D 825 MET cc_start: 0.3845 (mtt) cc_final: 0.3347 (mtt) REVERT: E 25 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.6935 (mm-30) REVERT: E 46 ARG cc_start: 0.8089 (tpp80) cc_final: 0.7839 (tpp80) REVERT: E 48 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8193 (tp30) REVERT: E 83 TYR cc_start: 0.7762 (m-80) cc_final: 0.7519 (m-10) REVERT: E 109 ARG cc_start: 0.6991 (mtt-85) cc_final: 0.6482 (mpt180) outliers start: 54 outliers final: 45 residues processed: 238 average time/residue: 0.7392 time to fit residues: 251.7128 Evaluate side-chains 237 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 187 time to evaluate : 2.762 ------------------------------------------------------------------------------- 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 328 TRP Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 392 HIS Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 480 CYS 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 813 ASP Chi-restraints excluded: chain B residue 21 GLN Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 110 CYS 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 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 426 ASP Chi-restraints excluded: chain D residue 483 ILE 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 648 PHE Chi-restraints excluded: chain D residue 653 ASP Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 63 ASP 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 233 HIS Chi-restraints excluded: chain F residue 246 MET Chi-restraints excluded: chain F residue 263 ASN 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 190 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 112 optimal weight: 0.6980 chunk 144 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 166 optimal weight: 7.9990 chunk 110 optimal weight: 0.7980 chunk 196 optimal weight: 20.0000 chunk 123 optimal weight: 0.6980 chunk 119 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6606 moved from start: 0.8860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17080 Z= 0.190 Angle : 0.534 7.179 23082 Z= 0.285 Chirality : 0.038 0.148 2520 Planarity : 0.004 0.047 3002 Dihedral : 4.477 53.027 2285 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.19 % Allowed : 15.28 % Favored : 81.52 % 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: 0.04 (0.19), residues: 2034 helix: 0.64 (0.16), residues: 986 sheet: -0.94 (0.37), residues: 210 loop : -0.30 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 139 HIS 0.002 0.001 HIS A 632 PHE 0.017 0.001 PHE A 482 TYR 0.017 0.001 TYR B 50 ARG 0.004 0.000 ARG B 47 *********************** 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 261 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 201 time to evaluate : 2.694 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: A 495 TYR cc_start: 0.6800 (OUTLIER) cc_final: 0.6398 (t80) REVERT: A 511 TYR cc_start: 0.5360 (OUTLIER) cc_final: 0.2585 (m-80) REVERT: A 573 GLU cc_start: 0.8989 (tt0) cc_final: 0.8038 (tp30) REVERT: A 635 MET cc_start: 0.7378 (mmm) cc_final: 0.7135 (ttm) REVERT: A 680 PHE cc_start: 0.8776 (m-80) cc_final: 0.8549 (m-10) REVERT: A 693 MET cc_start: 0.6723 (mmm) cc_final: 0.6480 (mmm) REVERT: A 825 MET cc_start: 0.3338 (mtt) cc_final: 0.2779 (mtt) REVERT: B 83 TYR cc_start: 0.7994 (m-80) cc_final: 0.7731 (m-10) REVERT: B 109 ARG cc_start: 0.6959 (mpt180) cc_final: 0.6408 (mmt-90) REVERT: C 243 MET cc_start: 0.8578 (mtp) cc_final: 0.7665 (mpp) REVERT: D 339 MET cc_start: 0.7609 (mtt) cc_final: 0.7234 (mtt) REVERT: D 366 ASP cc_start: 0.7419 (m-30) cc_final: 0.6915 (t70) REVERT: D 374 CYS cc_start: 0.8296 (m) cc_final: 0.6870 (m) REVERT: D 440 ARG cc_start: 0.3804 (tpm170) cc_final: 0.3384 (tpt170) REVERT: D 476 SER cc_start: 0.8513 (t) cc_final: 0.8062 (p) REVERT: D 495 TYR cc_start: 0.6917 (OUTLIER) cc_final: 0.6577 (t80) REVERT: D 511 TYR cc_start: 0.5492 (OUTLIER) cc_final: 0.3339 (m-80) REVERT: D 545 MET cc_start: 0.8194 (tpp) cc_final: 0.7867 (tpp) REVERT: D 618 VAL cc_start: 0.8490 (t) cc_final: 0.8109 (p) REVERT: D 680 PHE cc_start: 0.8388 (m-80) cc_final: 0.8143 (m-10) REVERT: D 825 MET cc_start: 0.3792 (mtt) cc_final: 0.3314 (mtt) REVERT: E 25 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7473 (mm-30) REVERT: E 46 ARG cc_start: 0.8007 (tpp80) cc_final: 0.7804 (tpp-160) REVERT: E 48 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8180 (tp30) REVERT: E 109 ARG cc_start: 0.6861 (mtt-85) cc_final: 0.6268 (mtt90) outliers start: 60 outliers final: 49 residues processed: 245 average time/residue: 0.7464 time to fit residues: 261.5324 Evaluate side-chains 245 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 191 time to evaluate : 2.647 ------------------------------------------------------------------------------- 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 291 MET Chi-restraints excluded: chain A residue 328 TRP Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 480 CYS 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 710 ARG Chi-restraints excluded: chain A residue 723 ASN Chi-restraints excluded: chain A residue 813 ASP Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 110 CYS 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 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 426 ASP Chi-restraints excluded: chain D residue 483 ILE Chi-restraints excluded: chain D residue 495 TYR Chi-restraints excluded: chain D residue 503 SER 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 525 LEU 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 E residue 25 GLU Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 63 ASP 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 233 HIS Chi-restraints excluded: chain F residue 246 MET Chi-restraints excluded: chain F residue 263 ASN 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 121 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 59 optimal weight: 30.0000 chunk 38 optimal weight: 7.9990 chunk 125 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 178 optimal weight: 3.9990 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 A 393 ASN ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 0.9328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17080 Z= 0.239 Angle : 0.564 6.569 23082 Z= 0.306 Chirality : 0.039 0.154 2520 Planarity : 0.004 0.046 3002 Dihedral : 4.569 51.706 2285 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 3.46 % Allowed : 15.65 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.01 (0.19), residues: 2034 helix: 0.60 (0.16), residues: 988 sheet: -1.02 (0.37), residues: 210 loop : -0.31 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 791 HIS 0.004 0.001 HIS A 632 PHE 0.015 0.002 PHE A 612 TYR 0.021 0.002 TYR B 50 ARG 0.005 0.001 ARG E 15 *********************** 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 253 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 188 time to evaluate : 2.632 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 135 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7045 (mm-30) REVERT: A 339 MET cc_start: 0.7868 (mtt) cc_final: 0.7661 (mtt) REVERT: A 495 TYR cc_start: 0.6976 (OUTLIER) cc_final: 0.6506 (t80) REVERT: A 511 TYR cc_start: 0.5261 (OUTLIER) cc_final: 0.2715 (m-80) REVERT: A 573 GLU cc_start: 0.9035 (tt0) cc_final: 0.8059 (tp30) REVERT: A 693 MET cc_start: 0.6744 (mmm) cc_final: 0.6472 (mmm) REVERT: A 825 MET cc_start: 0.3366 (mtt) cc_final: 0.2797 (mtt) REVERT: B 25 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7814 (mm-30) REVERT: B 109 ARG cc_start: 0.6908 (mpt180) cc_final: 0.6350 (mmt-90) REVERT: C 243 MET cc_start: 0.8641 (mtp) cc_final: 0.7716 (mpp) REVERT: C 282 ARG cc_start: 0.6570 (ttt-90) cc_final: 0.6363 (ttt-90) REVERT: D 366 ASP cc_start: 0.7628 (OUTLIER) cc_final: 0.7074 (t70) REVERT: D 440 ARG cc_start: 0.4026 (tpm170) cc_final: 0.3642 (tpt170) REVERT: D 476 SER cc_start: 0.8347 (t) cc_final: 0.7987 (p) REVERT: D 495 TYR cc_start: 0.6972 (OUTLIER) cc_final: 0.6623 (t80) REVERT: D 511 TYR cc_start: 0.5603 (OUTLIER) cc_final: 0.3598 (m-80) REVERT: D 545 MET cc_start: 0.8235 (tpp) cc_final: 0.7901 (tpp) REVERT: D 618 VAL cc_start: 0.8519 (t) cc_final: 0.8183 (p) REVERT: D 825 MET cc_start: 0.3778 (mtt) cc_final: 0.3282 (mtt) REVERT: E 46 ARG cc_start: 0.8014 (tpp80) cc_final: 0.7787 (tpp-160) REVERT: E 83 TYR cc_start: 0.7935 (m-80) cc_final: 0.7658 (m-10) outliers start: 65 outliers final: 53 residues processed: 236 average time/residue: 0.7675 time to fit residues: 258.8856 Evaluate side-chains 236 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 177 time to evaluate : 2.784 ------------------------------------------------------------------------------- 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 291 MET Chi-restraints excluded: chain A residue 328 TRP Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 480 CYS 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 710 ARG Chi-restraints excluded: chain A residue 723 ASN Chi-restraints excluded: chain A residue 813 ASP Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 125 HIS Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain C residue 194 LEU 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 275 ASN Chi-restraints excluded: chain D residue 279 ARG Chi-restraints excluded: chain D residue 328 TRP Chi-restraints excluded: chain D residue 366 ASP Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain D residue 483 ILE Chi-restraints excluded: chain D residue 495 TYR Chi-restraints excluded: chain D residue 503 SER 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 723 ASN Chi-restraints excluded: chain D residue 861 ARG Chi-restraints excluded: chain E residue 63 ASP 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 233 HIS Chi-restraints excluded: chain F residue 246 MET Chi-restraints excluded: chain F residue 263 ASN 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 188 optimal weight: 5.9990 chunk 171 optimal weight: 1.9990 chunk 183 optimal weight: 6.9990 chunk 110 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 143 optimal weight: 7.9990 chunk 56 optimal weight: 1.9990 chunk 165 optimal weight: 20.0000 chunk 173 optimal weight: 2.9990 chunk 182 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6671 moved from start: 0.9533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17080 Z= 0.218 Angle : 0.542 6.794 23082 Z= 0.291 Chirality : 0.039 0.148 2520 Planarity : 0.004 0.047 3002 Dihedral : 4.457 52.278 2285 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.04 % Allowed : 16.56 % Favored : 80.40 % 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: 0.09 (0.19), residues: 2034 helix: 0.70 (0.16), residues: 986 sheet: -1.01 (0.36), residues: 210 loop : -0.26 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 139 HIS 0.005 0.001 HIS B 31 PHE 0.015 0.001 PHE E 76 TYR 0.024 0.001 TYR B 50 ARG 0.004 0.000 ARG A 734 *********************** 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 243 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 186 time to evaluate : 2.648 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: A 135 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7066 (mm-30) REVERT: A 495 TYR cc_start: 0.6947 (OUTLIER) cc_final: 0.6495 (t80) REVERT: A 511 TYR cc_start: 0.5304 (OUTLIER) cc_final: 0.2989 (m-80) REVERT: A 573 GLU cc_start: 0.9021 (tt0) cc_final: 0.8065 (tp30) REVERT: A 693 MET cc_start: 0.6750 (mmm) cc_final: 0.6494 (mmm) REVERT: A 825 MET cc_start: 0.3331 (mtt) cc_final: 0.2768 (mtt) REVERT: B 25 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7887 (mm-30) REVERT: B 48 GLU cc_start: 0.8986 (mt-10) cc_final: 0.8012 (tp30) REVERT: B 109 ARG cc_start: 0.6926 (mpt180) cc_final: 0.6367 (mmt-90) REVERT: C 194 LEU cc_start: 0.6139 (OUTLIER) cc_final: 0.5551 (pt) REVERT: C 243 MET cc_start: 0.8657 (mtp) cc_final: 0.7787 (mpp) REVERT: C 280 ARG cc_start: 0.7388 (ttp-170) cc_final: 0.7135 (tpt-90) REVERT: C 282 ARG cc_start: 0.6660 (ttt-90) cc_final: 0.6435 (ttt-90) REVERT: D 366 ASP cc_start: 0.7545 (m-30) cc_final: 0.6957 (t70) REVERT: D 374 CYS cc_start: 0.8350 (m) cc_final: 0.7026 (m) REVERT: D 440 ARG cc_start: 0.4230 (tpm170) cc_final: 0.3795 (tpt170) REVERT: D 476 SER cc_start: 0.8327 (t) cc_final: 0.7969 (p) REVERT: D 488 THR cc_start: 0.8237 (m) cc_final: 0.7965 (p) REVERT: D 495 TYR cc_start: 0.6930 (OUTLIER) cc_final: 0.6586 (t80) REVERT: D 511 TYR cc_start: 0.5417 (OUTLIER) cc_final: 0.3582 (m-80) REVERT: D 545 MET cc_start: 0.8232 (tpp) cc_final: 0.7901 (tpp) REVERT: D 618 VAL cc_start: 0.8528 (t) cc_final: 0.8213 (p) REVERT: D 680 PHE cc_start: 0.8472 (m-80) cc_final: 0.8237 (m-10) REVERT: D 825 MET cc_start: 0.3701 (mtt) cc_final: 0.3234 (mtt) REVERT: E 47 ARG cc_start: 0.7906 (mmt180) cc_final: 0.7572 (mpt180) REVERT: E 48 GLU cc_start: 0.8781 (mt-10) cc_final: 0.8340 (tp30) REVERT: F 169 MET cc_start: 0.8418 (mtp) cc_final: 0.8150 (ptm) outliers start: 57 outliers final: 48 residues processed: 230 average time/residue: 0.7850 time to fit residues: 261.9185 Evaluate side-chains 234 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 180 time to evaluate : 3.626 ------------------------------------------------------------------------------- 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 291 MET Chi-restraints excluded: chain A residue 328 TRP Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 480 CYS 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 A residue 813 ASP Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 125 HIS Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain C residue 194 LEU 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 426 ASP Chi-restraints excluded: chain D residue 483 ILE Chi-restraints excluded: chain D residue 495 TYR Chi-restraints excluded: chain D residue 503 SER 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 723 ASN Chi-restraints excluded: chain E residue 63 ASP 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 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 193 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 91 optimal weight: 9.9990 chunk 134 optimal weight: 8.9990 chunk 203 optimal weight: 6.9990 chunk 187 optimal weight: 6.9990 chunk 161 optimal weight: 30.0000 chunk 16 optimal weight: 0.6980 chunk 125 optimal weight: 2.9990 chunk 99 optimal weight: 9.9990 chunk 128 optimal weight: 0.9980 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6700 moved from start: 0.9852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17080 Z= 0.232 Angle : 0.560 6.817 23082 Z= 0.301 Chirality : 0.039 0.149 2520 Planarity : 0.004 0.048 3002 Dihedral : 4.493 51.497 2285 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 3.14 % Allowed : 16.45 % Favored : 80.40 % 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: 0.08 (0.19), residues: 2034 helix: 0.70 (0.16), residues: 986 sheet: -1.01 (0.36), residues: 210 loop : -0.28 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 139 HIS 0.004 0.001 HIS B 85 PHE 0.017 0.002 PHE B 54 TYR 0.029 0.002 TYR B 50 ARG 0.005 0.001 ARG A 710 ********************** 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 245 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 186 time to evaluate : 2.965 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: A 135 GLU cc_start: 0.7660 (mt-10) cc_final: 0.7124 (mm-30) REVERT: A 495 TYR cc_start: 0.6970 (OUTLIER) cc_final: 0.6508 (t80) REVERT: A 511 TYR cc_start: 0.5246 (OUTLIER) cc_final: 0.3090 (m-80) REVERT: A 825 MET cc_start: 0.3323 (mtt) cc_final: 0.2782 (mtt) REVERT: B 48 GLU cc_start: 0.8987 (mt-10) cc_final: 0.8060 (tp30) REVERT: B 109 ARG cc_start: 0.6998 (mpt180) cc_final: 0.6425 (mmt-90) REVERT: C 194 LEU cc_start: 0.6103 (OUTLIER) cc_final: 0.5529 (pt) REVERT: C 243 MET cc_start: 0.8688 (mtp) cc_final: 0.7886 (mpp) REVERT: C 280 ARG cc_start: 0.7389 (ttp-170) cc_final: 0.6981 (tpp-160) REVERT: C 282 ARG cc_start: 0.6719 (ttt-90) cc_final: 0.6433 (ttt-90) REVERT: D 366 ASP cc_start: 0.7596 (OUTLIER) cc_final: 0.7031 (t70) REVERT: D 374 CYS cc_start: 0.8395 (m) cc_final: 0.7048 (m) REVERT: D 440 ARG cc_start: 0.4464 (tpm170) cc_final: 0.4230 (tpt170) REVERT: D 476 SER cc_start: 0.8352 (t) cc_final: 0.7996 (p) REVERT: D 495 TYR cc_start: 0.6904 (OUTLIER) cc_final: 0.6562 (t80) REVERT: D 511 TYR cc_start: 0.5392 (OUTLIER) cc_final: 0.3751 (m-80) REVERT: D 545 MET cc_start: 0.8248 (tpp) cc_final: 0.7911 (tpp) REVERT: D 550 ASP cc_start: 0.7557 (m-30) cc_final: 0.7336 (t70) REVERT: D 618 VAL cc_start: 0.8542 (t) cc_final: 0.8261 (p) REVERT: D 825 MET cc_start: 0.3628 (mtt) cc_final: 0.3160 (mtt) REVERT: E 47 ARG cc_start: 0.7851 (mmt180) cc_final: 0.7558 (mpt180) REVERT: E 48 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8354 (tp30) REVERT: F 169 MET cc_start: 0.8415 (mtp) cc_final: 0.8168 (ptm) outliers start: 59 outliers final: 47 residues processed: 231 average time/residue: 0.7566 time to fit residues: 248.4341 Evaluate side-chains 233 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 180 time to evaluate : 2.747 ------------------------------------------------------------------------------- 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 291 MET Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 426 ASP Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 480 CYS 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 A residue 813 ASP Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 110 CYS Chi-restraints excluded: chain B residue 125 HIS Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain C residue 194 LEU 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 366 ASP Chi-restraints excluded: chain D residue 426 ASP Chi-restraints excluded: chain D residue 483 ILE Chi-restraints excluded: chain D residue 495 TYR Chi-restraints excluded: chain D residue 503 SER 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 723 ASN Chi-restraints excluded: chain D residue 861 ARG Chi-restraints excluded: chain E residue 63 ASP 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 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 172 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 149 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 44 optimal weight: 0.4980 chunk 162 optimal weight: 30.0000 chunk 67 optimal weight: 20.0000 chunk 166 optimal weight: 8.9990 chunk 20 optimal weight: 9.9990 chunk 29 optimal weight: 0.7980 chunk 142 optimal weight: 6.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 233 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.161212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.129171 restraints weight = 141608.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.130070 restraints weight = 92621.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.130834 restraints weight = 66630.215| |-----------------------------------------------------------------------------| r_work (final): 0.4108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6785 moved from start: 0.9888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17080 Z= 0.164 Angle : 0.520 7.042 23082 Z= 0.272 Chirality : 0.038 0.148 2520 Planarity : 0.004 0.049 3002 Dihedral : 4.200 46.114 2285 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.45 % Allowed : 17.04 % Favored : 80.51 % 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: 0.50 (0.19), residues: 2034 helix: 1.06 (0.17), residues: 984 sheet: -0.91 (0.36), residues: 210 loop : -0.06 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 139 HIS 0.003 0.001 HIS F 233 PHE 0.016 0.001 PHE A 482 TYR 0.023 0.001 TYR B 50 ARG 0.011 0.000 ARG A 710 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6737.40 seconds wall clock time: 120 minutes 7.78 seconds (7207.78 seconds total)