Starting phenix.real_space_refine on Fri May 30 08:02:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r1g_18810/05_2025/8r1g_18810.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r1g_18810/05_2025/8r1g_18810.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8r1g_18810/05_2025/8r1g_18810.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r1g_18810/05_2025/8r1g_18810.map" model { file = "/net/cci-nas-00/data/ceres_data/8r1g_18810/05_2025/8r1g_18810.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r1g_18810/05_2025/8r1g_18810.cif" } resolution = 3.99 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.092 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 6 6.06 5 S 112 5.16 5 C 10610 2.51 5 N 2862 2.21 5 O 3142 1.98 5 H 16526 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 33258 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 11110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 681, 11110 Classifications: {'peptide': 681} Link IDs: {'PTRANS': 28, 'TRANS': 652} Chain breaks: 1 Chain: "B" Number of atoms: 2365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 2365 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "C" Number of atoms: 3151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 3151 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 15, 'TRANS': 186} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12835 SG CYS B 110 73.866 102.944 46.248 1.00 88.62 S ATOM 12878 SG CYS B 113 74.283 103.712 42.874 1.00 87.95 S ATOM 13405 SG CYS B 143 76.342 100.773 44.385 1.00 87.19 S ATOM 13429 SG CYS B 146 77.307 104.282 45.198 1.00 93.27 S ATOM 11605 SG CYS B 37 66.178 114.896 36.868 1.00114.45 S ATOM 11652 SG CYS B 40 67.616 118.161 36.171 1.00108.22 S ATOM 12158 SG CYS B 70 69.841 114.908 36.696 1.00103.60 S ATOM 12202 SG CYS B 73 68.199 116.574 39.588 1.00 99.17 S ATOM 14814 SG CYS C 176 65.958 71.313 19.330 1.00187.28 S ATOM 15777 SG CYS C 238 64.381 73.597 22.216 1.00182.95 S ATOM 15823 SG CYS C 242 68.011 73.982 21.267 1.00171.60 S Restraints were copied for chains: F, D, E Time building chain proxies: 39.64, per 1000 atoms: 1.19 Number of scatterers: 33258 At special positions: 0 Unit cell: (159.6, 152.88, 122.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 6 29.99 S 112 16.00 O 3142 8.00 N 2862 7.00 C 10610 6.00 H 16526 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.64 Conformation dependent library (CDL) restraints added in 2.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 201 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 110 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 143 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 146 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 113 " pdb=" ZN B 202 " pdb="ZN ZN B 202 " - pdb=" SG CYS B 37 " pdb="ZN ZN B 202 " - pdb=" SG CYS B 40 " pdb="ZN ZN B 202 " - pdb=" SG CYS B 73 " pdb="ZN ZN B 202 " - pdb=" SG CYS B 70 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" ND1 HIS C 179 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 238 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 176 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 242 " pdb=" ZN E 201 " pdb="ZN ZN E 201 " - pdb=" SG CYS E 110 " pdb="ZN ZN E 201 " - pdb=" SG CYS E 113 " pdb="ZN ZN E 201 " - pdb=" SG CYS E 143 " pdb="ZN ZN E 201 " - pdb=" SG CYS E 146 " pdb=" ZN E 202 " pdb="ZN ZN E 202 " - pdb=" SG CYS E 37 " pdb="ZN ZN E 202 " - pdb=" SG CYS E 40 " pdb="ZN ZN E 202 " - pdb=" SG CYS E 73 " pdb="ZN ZN E 202 " - pdb=" SG CYS E 70 " pdb=" ZN F 401 " pdb="ZN ZN F 401 " - pdb=" ND1 HIS F 179 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 238 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 176 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 242 " Number of angles added : 30 4068 Ramachandran restraints generated. 2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3904 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 18 sheets defined 56.4% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.51 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: 11.70 Time building geometry restraints manager: 9.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 16490 1.03 - 1.23: 209 1.23 - 1.43: 7003 1.43 - 1.63: 9738 1.63 - 1.82: 166 Bond restraints: 33606 Sorted by residual: bond pdb=" N VAL D 234 " pdb=" H VAL D 234 " ideal model delta sigma weight residual 0.860 0.962 -0.102 2.00e-02 2.50e+03 2.58e+01 bond pdb=" N VAL A 234 " pdb=" H VAL A 234 " ideal model delta sigma weight residual 0.860 0.961 -0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" CB ASN A 258 " pdb=" CG ASN A 258 " ideal model delta sigma weight residual 1.516 1.460 0.056 2.50e-02 1.60e+03 4.93e+00 bond pdb=" CE LYS D 311 " pdb=" NZ LYS D 311 " ideal model delta sigma weight residual 1.489 1.426 0.063 3.00e-02 1.11e+03 4.46e+00 bond pdb=" C ILE A 401 " pdb=" N PRO A 402 " ideal model delta sigma weight residual 1.330 1.354 -0.024 1.25e-02 6.40e+03 3.82e+00 ... (remaining 33601 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 57716 1.75 - 3.50: 2766 3.50 - 5.24: 175 5.24 - 6.99: 25 6.99 - 8.74: 6 Bond angle restraints: 60688 Sorted by residual: angle pdb=" CB ARG A 500 " pdb=" CG ARG A 500 " pdb=" CD ARG A 500 " ideal model delta sigma weight residual 111.30 102.62 8.68 2.30e+00 1.89e-01 1.42e+01 angle pdb=" CB ARG D 500 " pdb=" CG ARG D 500 " pdb=" CD ARG D 500 " ideal model delta sigma weight residual 111.30 102.66 8.64 2.30e+00 1.89e-01 1.41e+01 angle pdb=" C GLU A 135 " pdb=" CA GLU A 135 " pdb=" CB GLU A 135 " ideal model delta sigma weight residual 110.46 103.63 6.83 1.94e+00 2.66e-01 1.24e+01 angle pdb=" C GLU D 135 " pdb=" CA GLU D 135 " pdb=" CB GLU D 135 " ideal model delta sigma weight residual 110.46 103.64 6.82 1.94e+00 2.66e-01 1.24e+01 angle pdb=" C PHE D 256 " pdb=" CA PHE D 256 " pdb=" CB PHE D 256 " ideal model delta sigma weight residual 110.88 106.15 4.73 1.57e+00 4.06e-01 9.07e+00 ... (remaining 60683 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.92: 14271 15.92 - 31.85: 918 31.85 - 47.77: 315 47.77 - 63.70: 258 63.70 - 79.62: 70 Dihedral angle restraints: 15832 sinusoidal: 8702 harmonic: 7130 Sorted by residual: dihedral pdb=" CD ARG A 500 " pdb=" NE ARG A 500 " pdb=" CZ ARG A 500 " pdb=" NH1 ARG A 500 " ideal model delta sinusoidal sigma weight residual 0.00 36.47 -36.47 1 1.00e+01 1.00e-02 1.88e+01 dihedral pdb=" CD ARG D 500 " pdb=" NE ARG D 500 " pdb=" CZ ARG D 500 " pdb=" NH1 ARG D 500 " ideal model delta sinusoidal sigma weight residual 0.00 36.40 -36.40 1 1.00e+01 1.00e-02 1.87e+01 dihedral pdb=" CA ASN D 723 " pdb=" C ASN D 723 " pdb=" N LYS D 724 " pdb=" CA LYS D 724 " ideal model delta harmonic sigma weight residual -180.00 -160.87 -19.13 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 15829 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1591 0.053 - 0.107: 635 0.107 - 0.160: 247 0.160 - 0.213: 38 0.213 - 0.267: 9 Chirality restraints: 2520 Sorted by residual: chirality pdb=" CA ASN A 699 " pdb=" N ASN A 699 " pdb=" C ASN A 699 " pdb=" CB ASN A 699 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CA ASN D 699 " pdb=" N ASN D 699 " pdb=" C ASN D 699 " pdb=" CB ASN D 699 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA ARG F 248 " pdb=" N ARG F 248 " pdb=" C ARG F 248 " pdb=" CB ARG F 248 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 2517 not shown) Planarity restraints: 4944 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 500 " 0.754 9.50e-02 1.11e+02 2.52e-01 6.95e+01 pdb=" NE ARG A 500 " -0.024 2.00e-02 2.50e+03 pdb=" CZ ARG A 500 " -0.041 2.00e-02 2.50e+03 pdb=" NH1 ARG A 500 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 500 " 0.008 2.00e-02 2.50e+03 pdb="HH11 ARG A 500 " -0.006 2.00e-02 2.50e+03 pdb="HH12 ARG A 500 " 0.006 2.00e-02 2.50e+03 pdb="HH21 ARG A 500 " 0.004 2.00e-02 2.50e+03 pdb="HH22 ARG A 500 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 500 " -0.754 9.50e-02 1.11e+02 2.52e-01 6.95e+01 pdb=" NE ARG D 500 " 0.024 2.00e-02 2.50e+03 pdb=" CZ ARG D 500 " 0.041 2.00e-02 2.50e+03 pdb=" NH1 ARG D 500 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG D 500 " -0.008 2.00e-02 2.50e+03 pdb="HH11 ARG D 500 " 0.006 2.00e-02 2.50e+03 pdb="HH12 ARG D 500 " -0.006 2.00e-02 2.50e+03 pdb="HH21 ARG D 500 " -0.004 2.00e-02 2.50e+03 pdb="HH22 ARG D 500 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 734 " -0.380 9.50e-02 1.11e+02 1.27e-01 1.73e+01 pdb=" NE ARG A 734 " 0.020 2.00e-02 2.50e+03 pdb=" CZ ARG A 734 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 734 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 734 " -0.004 2.00e-02 2.50e+03 pdb="HH11 ARG A 734 " 0.006 2.00e-02 2.50e+03 pdb="HH12 ARG A 734 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG A 734 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 734 " -0.004 2.00e-02 2.50e+03 ... (remaining 4941 not shown) Histogram of nonbonded interaction distances: 1.22 - 1.90: 179 1.90 - 2.57: 31111 2.57 - 3.25: 104416 3.25 - 3.92: 126028 3.92 - 4.60: 201555 Nonbonded interactions: 463289 Sorted by model distance: nonbonded pdb=" OH TYR A 262 " pdb=" HZ3 LYS D 311 " model vdw 1.223 2.450 nonbonded pdb=" OH TYR A 262 " pdb=" HZ1 LYS D 311 " model vdw 1.543 2.450 nonbonded pdb=" OH TYR A 262 " pdb=" NZ LYS D 311 " model vdw 1.603 2.950 nonbonded pdb=" OE2 GLU A 130 " pdb=" HH TYR A 134 " model vdw 1.680 2.450 nonbonded pdb=" OE2 GLU D 130 " pdb=" HH TYR D 134 " model vdw 1.681 2.450 ... (remaining 463284 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.09 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'F' } ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 0.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.570 Extract box with map and model: 1.110 Check model and map are aligned: 0.220 Set scattering table: 0.270 Process input model: 98.260 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5536 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 17104 Z= 0.313 Angle : 0.940 11.619 23112 Z= 0.534 Chirality : 0.065 0.267 2520 Planarity : 0.014 0.326 3002 Dihedral : 11.486 79.623 6542 Min Nonbonded Distance : 1.603 Molprobity Statistics. All-atom Clashscore : 1.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.27 % Allowed : 2.45 % Favored : 97.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.17), residues: 2034 helix: -0.79 (0.15), residues: 964 sheet: -0.26 (0.33), residues: 236 loop : 0.14 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP D 791 HIS 0.011 0.002 HIS F 233 PHE 0.043 0.004 PHE D 256 TYR 0.033 0.004 TYR A 494 ARG 0.028 0.001 ARG D 500 Details of bonding type rmsd hydrogen bonds : bond 0.13804 ( 844) hydrogen bonds : angle 7.32616 ( 2352) metal coordination : bond 0.02257 ( 24) metal coordination : angle 5.25689 ( 30) covalent geometry : bond 0.00616 (17080) covalent geometry : angle 0.92106 (23082) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4068 Ramachandran restraints generated. 2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4068 Ramachandran restraints generated. 2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Residue MET 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Evaluate side-chains 473 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 468 time to evaluate : 2.569 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: 0.8059 time to fit residues: 528.4489 Evaluate side-chains 272 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 271 time to evaluate : 2.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 503 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 1.9990 chunk 154 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 159 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 chunk 119 optimal weight: 0.8980 chunk 185 optimal weight: 9.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 31 HIS B 98 GLN ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 795 HIS E 21 GLN E 98 GLN E 114 GLN F 131 ASN ** F 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 167 GLN F 288 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4779 r_free = 0.4779 target = 0.174975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.141442 restraints weight = 146765.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.145744 restraints weight = 79309.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.149040 restraints weight = 54684.616| |-----------------------------------------------------------------------------| r_work (final): 0.4423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6191 moved from start: 0.4624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 17104 Z= 0.233 Angle : 0.706 12.288 23112 Z= 0.382 Chirality : 0.042 0.181 2520 Planarity : 0.006 0.079 3002 Dihedral : 4.760 37.899 2285 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.40 % Allowed : 8.04 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.18), residues: 2034 helix: 0.31 (0.16), residues: 980 sheet: -0.70 (0.34), residues: 234 loop : 0.13 (0.22), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 791 HIS 0.007 0.002 HIS B 85 PHE 0.026 0.002 PHE B 52 TYR 0.028 0.002 TYR B 67 ARG 0.007 0.001 ARG D 155 Details of bonding type rmsd hydrogen bonds : bond 0.05312 ( 844) hydrogen bonds : angle 5.80221 ( 2352) metal coordination : bond 0.02293 ( 24) metal coordination : angle 3.65595 ( 30) covalent geometry : bond 0.00497 (17080) covalent geometry : angle 0.69438 (23082) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4068 Ramachandran restraints generated. 2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4068 Ramachandran restraints generated. 2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Residue MET 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Evaluate side-chains 316 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 271 time to evaluate : 2.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 495 TYR cc_start: 0.7099 (OUTLIER) cc_final: 0.6153 (t80) REVERT: A 545 MET cc_start: 0.6712 (tpp) cc_final: 0.6337 (tpp) REVERT: A 693 MET cc_start: 0.5646 (mmp) cc_final: 0.5360 (mmm) REVERT: A 825 MET cc_start: 0.2785 (mtt) cc_final: 0.2326 (mtt) REVERT: B 79 LYS cc_start: 0.7806 (tptt) cc_final: 0.7173 (ttmt) REVERT: C 243 MET cc_start: 0.7998 (mtp) cc_final: 0.7639 (mpp) REVERT: D 291 MET cc_start: 0.7747 (mmm) cc_final: 0.7365 (tpp) REVERT: D 313 MET cc_start: 0.8774 (ttm) cc_final: 0.8472 (ttm) REVERT: D 339 MET cc_start: 0.7079 (mtm) cc_final: 0.6872 (mtt) REVERT: D 395 GLU cc_start: 0.6146 (mt-10) cc_final: 0.5919 (mp0) REVERT: D 488 THR cc_start: 0.8650 (m) cc_final: 0.8375 (p) REVERT: D 495 TYR cc_start: 0.7061 (OUTLIER) cc_final: 0.6375 (t80) REVERT: D 501 MET cc_start: 0.8391 (mtt) cc_final: 0.7664 (tmm) REVERT: D 540 LEU cc_start: 0.7531 (mt) cc_final: 0.7267 (mm) REVERT: D 550 ASP cc_start: 0.7516 (m-30) cc_final: 0.7208 (t70) REVERT: D 618 VAL cc_start: 0.7959 (t) cc_final: 0.7520 (p) REVERT: D 680 PHE cc_start: 0.7546 (m-80) cc_final: 0.7051 (m-80) REVERT: D 825 MET cc_start: 0.3432 (mtt) cc_final: 0.3105 (mtt) REVERT: F 120 LYS cc_start: 0.4358 (tttt) cc_final: 0.3980 (mtmt) REVERT: F 134 PHE cc_start: 0.4877 (m-80) cc_final: 0.4568 (m-80) REVERT: F 282 ARG cc_start: 0.6442 (ttt180) cc_final: 0.6131 (ttt180) outliers start: 45 outliers final: 28 residues processed: 302 average time/residue: 0.6956 time to fit residues: 306.0236 Evaluate side-chains 258 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 228 time to evaluate : 2.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 490 ASN Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 125 HIS Chi-restraints excluded: chain C residue 204 GLU Chi-restraints excluded: chain C residue 239 ASN Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 377 MET Chi-restraints excluded: chain D residue 495 TYR Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 522 TYR Chi-restraints excluded: chain D residue 653 ASP Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 233 HIS Chi-restraints excluded: chain F residue 263 ASN Chi-restraints excluded: chain F residue 289 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 163 optimal weight: 9.9990 chunk 110 optimal weight: 7.9990 chunk 167 optimal weight: 30.0000 chunk 29 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 178 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 chunk 187 optimal weight: 7.9990 chunk 179 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 625 ASN ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 ASN D 258 ASN ** E 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN ** F 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 165 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4757 r_free = 0.4757 target = 0.173431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.142806 restraints weight = 144204.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.145377 restraints weight = 81284.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.146058 restraints weight = 55422.180| |-----------------------------------------------------------------------------| r_work (final): 0.4321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6359 moved from start: 0.5679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17104 Z= 0.161 Angle : 0.589 5.175 23112 Z= 0.314 Chirality : 0.040 0.169 2520 Planarity : 0.005 0.041 3002 Dihedral : 4.394 33.926 2285 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.08 % Allowed : 9.80 % 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: 0.60 (0.19), residues: 2034 helix: 0.89 (0.16), residues: 984 sheet: -0.73 (0.33), residues: 240 loop : 0.37 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 139 HIS 0.006 0.001 HIS E 31 PHE 0.019 0.002 PHE D 713 TYR 0.023 0.002 TYR A 502 ARG 0.010 0.001 ARG D 528 Details of bonding type rmsd hydrogen bonds : bond 0.04371 ( 844) hydrogen bonds : angle 5.25489 ( 2352) metal coordination : bond 0.01350 ( 24) metal coordination : angle 2.24108 ( 30) covalent geometry : bond 0.00352 (17080) covalent geometry : angle 0.58333 (23082) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4068 Ramachandran restraints generated. 2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4068 Ramachandran restraints generated. 2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Residue MET 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Evaluate side-chains 284 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 245 time to evaluate : 2.531 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: A 163 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7923 (tt) REVERT: A 476 SER cc_start: 0.8409 (t) cc_final: 0.7842 (m) REVERT: A 495 TYR cc_start: 0.7189 (OUTLIER) cc_final: 0.6005 (t80) REVERT: A 545 MET cc_start: 0.6325 (tpp) cc_final: 0.6010 (tpp) REVERT: A 573 GLU cc_start: 0.8026 (tt0) cc_final: 0.7473 (tp30) REVERT: A 680 PHE cc_start: 0.7583 (m-80) cc_final: 0.7362 (m-80) REVERT: A 693 MET cc_start: 0.6574 (mmp) cc_final: 0.6363 (mmm) REVERT: A 825 MET cc_start: 0.3144 (mtt) cc_final: 0.2584 (mtt) REVERT: B 79 LYS cc_start: 0.7881 (tptt) cc_final: 0.7211 (ttmt) REVERT: B 109 ARG cc_start: 0.6592 (mpt180) cc_final: 0.6121 (mmt-90) REVERT: C 243 MET cc_start: 0.8388 (mtp) cc_final: 0.7714 (mpp) REVERT: D 163 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8433 (tt) REVERT: D 313 MET cc_start: 0.8606 (ttm) cc_final: 0.8307 (ttm) REVERT: D 339 MET cc_start: 0.7544 (mtm) cc_final: 0.7241 (mtt) REVERT: D 431 GLU cc_start: 0.6178 (tm-30) cc_final: 0.5848 (tm-30) REVERT: D 488 THR cc_start: 0.8509 (m) cc_final: 0.8188 (p) REVERT: D 495 TYR cc_start: 0.7232 (OUTLIER) cc_final: 0.6296 (t80) REVERT: D 542 MET cc_start: 0.8098 (mmp) cc_final: 0.7513 (ptm) REVERT: D 550 ASP cc_start: 0.7767 (m-30) cc_final: 0.7374 (t70) REVERT: D 618 VAL cc_start: 0.8109 (t) cc_final: 0.7784 (p) REVERT: D 680 PHE cc_start: 0.7991 (m-80) cc_final: 0.7541 (m-80) REVERT: F 120 LYS cc_start: 0.4697 (tttt) cc_final: 0.4316 (mtmt) REVERT: F 134 PHE cc_start: 0.5202 (m-80) cc_final: 0.4566 (m-80) outliers start: 39 outliers final: 19 residues processed: 271 average time/residue: 0.7988 time to fit residues: 307.1985 Evaluate side-chains 231 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 208 time to evaluate : 2.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain C residue 239 ASN Chi-restraints excluded: chain D residue 151 ARG Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 495 TYR Chi-restraints excluded: chain D residue 522 TYR Chi-restraints excluded: chain D residue 653 ASP Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain F residue 233 HIS Chi-restraints excluded: chain F residue 239 ASN Chi-restraints excluded: chain F residue 263 ASN Chi-restraints excluded: chain F residue 289 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 37 optimal weight: 0.8980 chunk 116 optimal weight: 0.9990 chunk 52 optimal weight: 7.9990 chunk 109 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 158 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 137 optimal weight: 2.9990 chunk 122 optimal weight: 9.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 ASN ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN ** F 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4757 r_free = 0.4757 target = 0.172700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.141258 restraints weight = 147438.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.143362 restraints weight = 84117.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.145009 restraints weight = 64100.422| |-----------------------------------------------------------------------------| r_work (final): 0.4320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6419 moved from start: 0.6213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17104 Z= 0.118 Angle : 0.526 4.951 23112 Z= 0.275 Chirality : 0.038 0.157 2520 Planarity : 0.004 0.042 3002 Dihedral : 4.123 19.249 2284 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.70 % Allowed : 10.81 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.88 (0.19), residues: 2034 helix: 1.14 (0.17), residues: 984 sheet: -0.61 (0.33), residues: 240 loop : 0.48 (0.23), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 139 HIS 0.002 0.001 HIS D 632 PHE 0.014 0.001 PHE E 76 TYR 0.014 0.001 TYR B 83 ARG 0.005 0.000 ARG D 506 Details of bonding type rmsd hydrogen bonds : bond 0.03752 ( 844) hydrogen bonds : angle 4.98707 ( 2352) metal coordination : bond 0.00766 ( 24) metal coordination : angle 2.18146 ( 30) covalent geometry : bond 0.00260 (17080) covalent geometry : angle 0.52077 (23082) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4068 Ramachandran restraints generated. 2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4068 Ramachandran restraints generated. 2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Residue MET 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Evaluate side-chains 259 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 227 time to evaluate : 2.584 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: A 163 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7718 (tt) REVERT: A 236 ILE cc_start: 0.6746 (OUTLIER) cc_final: 0.6415 (mp) REVERT: A 304 MET cc_start: 0.8145 (tpp) cc_final: 0.7813 (tpp) REVERT: A 476 SER cc_start: 0.8341 (t) cc_final: 0.7742 (m) REVERT: A 495 TYR cc_start: 0.6883 (OUTLIER) cc_final: 0.6035 (t80) REVERT: A 542 MET cc_start: 0.5290 (ptt) cc_final: 0.4880 (ptm) REVERT: A 545 MET cc_start: 0.6345 (tpp) cc_final: 0.6058 (tpp) REVERT: A 680 PHE cc_start: 0.7406 (m-80) cc_final: 0.6976 (m-80) REVERT: A 693 MET cc_start: 0.6747 (mmp) cc_final: 0.6398 (mmm) REVERT: A 825 MET cc_start: 0.3047 (mtt) cc_final: 0.2685 (mtt) REVERT: B 99 TYR cc_start: 0.6895 (m-80) cc_final: 0.6635 (m-80) REVERT: B 109 ARG cc_start: 0.6399 (mpt180) cc_final: 0.5889 (mmt-90) REVERT: C 243 MET cc_start: 0.8560 (mtp) cc_final: 0.7897 (mpp) REVERT: D 163 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8222 (tt) REVERT: D 313 MET cc_start: 0.8605 (ttm) cc_final: 0.8321 (ttm) REVERT: D 339 MET cc_start: 0.7348 (mtm) cc_final: 0.7052 (mtt) REVERT: D 488 THR cc_start: 0.8310 (m) cc_final: 0.8018 (p) REVERT: D 495 TYR cc_start: 0.7067 (OUTLIER) cc_final: 0.6231 (t80) REVERT: D 511 TYR cc_start: 0.5686 (OUTLIER) cc_final: 0.4071 (m-80) REVERT: D 542 MET cc_start: 0.7971 (mmp) cc_final: 0.7376 (ptm) REVERT: D 550 ASP cc_start: 0.7675 (m-30) cc_final: 0.7130 (t70) REVERT: D 618 VAL cc_start: 0.8059 (t) cc_final: 0.7758 (p) REVERT: D 642 MET cc_start: 0.8792 (mmt) cc_final: 0.8525 (mmm) REVERT: D 680 PHE cc_start: 0.8012 (m-80) cc_final: 0.7573 (m-80) REVERT: D 825 MET cc_start: 0.3404 (mtt) cc_final: 0.2901 (mtt) REVERT: F 120 LYS cc_start: 0.4746 (tttt) cc_final: 0.4355 (mtmt) REVERT: F 134 PHE cc_start: 0.4921 (m-80) cc_final: 0.4197 (m-80) REVERT: F 237 MET cc_start: -0.2563 (OUTLIER) cc_final: -0.3063 (mmt) outliers start: 32 outliers final: 22 residues processed: 250 average time/residue: 0.7754 time to fit residues: 274.0667 Evaluate side-chains 236 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 207 time to evaluate : 2.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain B residue 125 HIS Chi-restraints excluded: chain C residue 239 ASN Chi-restraints excluded: chain D residue 151 ARG Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 279 ARG Chi-restraints excluded: chain D residue 495 TYR Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 511 TYR Chi-restraints excluded: chain D residue 522 TYR Chi-restraints excluded: chain D residue 653 ASP Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain F residue 233 HIS Chi-restraints excluded: chain F residue 237 MET Chi-restraints excluded: chain F residue 239 ASN Chi-restraints excluded: chain F residue 289 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 154 optimal weight: 5.9990 chunk 152 optimal weight: 10.0000 chunk 60 optimal weight: 40.0000 chunk 5 optimal weight: 1.9990 chunk 102 optimal weight: 7.9990 chunk 49 optimal weight: 8.9990 chunk 3 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 chunk 178 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 197 optimal weight: 0.1980 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 625 ASN ** D 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN ** F 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.167780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.136565 restraints weight = 146117.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.137406 restraints weight = 88983.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.138396 restraints weight = 70695.883| |-----------------------------------------------------------------------------| r_work (final): 0.4213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6574 moved from start: 0.7002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17104 Z= 0.188 Angle : 0.568 5.218 23112 Z= 0.307 Chirality : 0.039 0.154 2520 Planarity : 0.005 0.053 3002 Dihedral : 4.288 20.765 2284 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.18 % Allowed : 11.29 % Favored : 86.53 % 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: 0.56 (0.19), residues: 2034 helix: 0.91 (0.16), residues: 988 sheet: -0.69 (0.33), residues: 240 loop : 0.25 (0.22), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 139 HIS 0.007 0.001 HIS E 85 PHE 0.015 0.002 PHE D 612 TYR 0.020 0.002 TYR A 494 ARG 0.009 0.001 ARG A 529 Details of bonding type rmsd hydrogen bonds : bond 0.04175 ( 844) hydrogen bonds : angle 5.19314 ( 2352) metal coordination : bond 0.01333 ( 24) metal coordination : angle 2.23129 ( 30) covalent geometry : bond 0.00399 (17080) covalent geometry : angle 0.56301 (23082) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4068 Ramachandran restraints generated. 2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4068 Ramachandran restraints generated. 2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Residue MET 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Evaluate side-chains 256 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 215 time to evaluate : 2.597 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: A 163 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7955 (tt) REVERT: A 413 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7570 (mt) REVERT: A 440 ARG cc_start: 0.3622 (tpm170) cc_final: 0.3069 (tpt170) REVERT: A 476 SER cc_start: 0.8427 (t) cc_final: 0.7941 (m) REVERT: A 495 TYR cc_start: 0.6977 (OUTLIER) cc_final: 0.6115 (t80) REVERT: A 511 TYR cc_start: 0.4824 (OUTLIER) cc_final: 0.2135 (m-80) REVERT: A 542 MET cc_start: 0.6334 (ptt) cc_final: 0.5928 (ptm) REVERT: A 573 GLU cc_start: 0.8597 (tt0) cc_final: 0.7642 (tp30) REVERT: A 577 LEU cc_start: 0.8632 (mm) cc_final: 0.8412 (mm) REVERT: A 680 PHE cc_start: 0.7670 (m-80) cc_final: 0.7217 (m-80) REVERT: A 693 MET cc_start: 0.6807 (mmp) cc_final: 0.6517 (mmm) REVERT: A 825 MET cc_start: 0.3203 (mtt) cc_final: 0.2685 (mtt) REVERT: B 109 ARG cc_start: 0.6491 (mpt180) cc_final: 0.6178 (mmt-90) REVERT: C 167 GLN cc_start: 0.6950 (pt0) cc_final: 0.6507 (pm20) REVERT: C 243 MET cc_start: 0.8554 (mtp) cc_final: 0.7868 (mpp) REVERT: D 163 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8408 (tt) REVERT: D 313 MET cc_start: 0.8798 (ttm) cc_final: 0.8559 (ttm) REVERT: D 339 MET cc_start: 0.7443 (mtm) cc_final: 0.7167 (mtt) REVERT: D 495 TYR cc_start: 0.7174 (OUTLIER) cc_final: 0.6419 (t80) REVERT: D 511 TYR cc_start: 0.5291 (OUTLIER) cc_final: 0.3213 (m-80) REVERT: D 525 LEU cc_start: 0.5551 (mt) cc_final: 0.5334 (mt) REVERT: D 542 MET cc_start: 0.8300 (mmp) cc_final: 0.7603 (ptt) REVERT: D 618 VAL cc_start: 0.8283 (t) cc_final: 0.7989 (p) REVERT: D 680 PHE cc_start: 0.8042 (m-80) cc_final: 0.7643 (m-80) REVERT: D 825 MET cc_start: 0.3419 (mtt) cc_final: 0.2911 (mtt) REVERT: F 120 LYS cc_start: 0.4065 (tttt) cc_final: 0.3755 (mtmt) outliers start: 41 outliers final: 27 residues processed: 245 average time/residue: 0.7828 time to fit residues: 274.1615 Evaluate side-chains 234 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 200 time to evaluate : 2.799 ------------------------------------------------------------------------------- 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 325 ILE Chi-restraints excluded: chain A residue 413 LEU 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 510 LEU Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 125 HIS Chi-restraints excluded: chain C residue 239 ASN Chi-restraints excluded: chain D residue 151 ARG Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 279 ARG Chi-restraints excluded: chain D residue 495 TYR Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 511 TYR Chi-restraints excluded: chain D residue 522 TYR Chi-restraints excluded: chain D residue 653 ASP Chi-restraints excluded: chain D residue 713 PHE Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain F residue 233 HIS Chi-restraints excluded: chain F residue 239 ASN Chi-restraints excluded: chain F residue 289 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 67 optimal weight: 20.0000 chunk 126 optimal weight: 1.9990 chunk 201 optimal weight: 10.0000 chunk 125 optimal weight: 2.9990 chunk 115 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 116 optimal weight: 0.5980 chunk 97 optimal weight: 0.7980 chunk 168 optimal weight: 30.0000 chunk 94 optimal weight: 20.0000 chunk 104 optimal weight: 7.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 HIS ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 GLN D 497 ASN ** D 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN E 114 GLN ** F 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4711 r_free = 0.4711 target = 0.170060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.137265 restraints weight = 145579.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.140166 restraints weight = 84035.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.141803 restraints weight = 58842.752| |-----------------------------------------------------------------------------| r_work (final): 0.4246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6508 moved from start: 0.7229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 17104 Z= 0.107 Angle : 0.508 6.179 23112 Z= 0.263 Chirality : 0.038 0.146 2520 Planarity : 0.004 0.048 3002 Dihedral : 3.998 18.545 2284 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.49 % Allowed : 12.67 % Favored : 85.84 % 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: 0.95 (0.19), residues: 2034 helix: 1.27 (0.17), residues: 988 sheet: -0.59 (0.33), residues: 240 loop : 0.41 (0.23), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 139 HIS 0.002 0.000 HIS D 632 PHE 0.016 0.001 PHE B 76 TYR 0.021 0.001 TYR B 83 ARG 0.005 0.000 ARG D 506 Details of bonding type rmsd hydrogen bonds : bond 0.03518 ( 844) hydrogen bonds : angle 4.83750 ( 2352) metal coordination : bond 0.00661 ( 24) metal coordination : angle 2.24912 ( 30) covalent geometry : bond 0.00236 (17080) covalent geometry : angle 0.50207 (23082) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4068 Ramachandran restraints generated. 2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4068 Ramachandran restraints generated. 2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Residue MET 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Evaluate side-chains 243 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 215 time to evaluate : 2.572 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: A 151 ARG cc_start: 0.7502 (OUTLIER) cc_final: 0.7043 (mmm160) REVERT: A 304 MET cc_start: 0.8286 (tpp) cc_final: 0.7886 (tpp) REVERT: A 440 ARG cc_start: 0.3358 (tpm170) cc_final: 0.2943 (tpt170) REVERT: A 476 SER cc_start: 0.8186 (t) cc_final: 0.7899 (m) REVERT: A 495 TYR cc_start: 0.7128 (OUTLIER) cc_final: 0.6164 (t80) REVERT: A 511 TYR cc_start: 0.5091 (OUTLIER) cc_final: 0.2310 (m-80) REVERT: A 680 PHE cc_start: 0.7629 (m-80) cc_final: 0.7153 (m-80) REVERT: A 693 MET cc_start: 0.6857 (mmp) cc_final: 0.6610 (mmm) REVERT: A 825 MET cc_start: 0.3034 (mtt) cc_final: 0.2704 (mtt) REVERT: B 99 TYR cc_start: 0.7105 (m-80) cc_final: 0.6711 (m-80) REVERT: B 109 ARG cc_start: 0.6425 (mpt180) cc_final: 0.5800 (mmt90) REVERT: C 167 GLN cc_start: 0.7051 (pt0) cc_final: 0.6595 (pm20) REVERT: C 243 MET cc_start: 0.8640 (mtp) cc_final: 0.7933 (mpp) REVERT: C 286 GLU cc_start: 0.8278 (mt-10) cc_final: 0.7694 (mt-10) REVERT: D 313 MET cc_start: 0.8656 (ttm) cc_final: 0.8360 (ttm) REVERT: D 339 MET cc_start: 0.7761 (mtm) cc_final: 0.7384 (mtt) REVERT: D 488 THR cc_start: 0.8325 (m) cc_final: 0.7964 (p) REVERT: D 495 TYR cc_start: 0.7379 (OUTLIER) cc_final: 0.6588 (t80) REVERT: D 511 TYR cc_start: 0.5307 (OUTLIER) cc_final: 0.3744 (m-80) REVERT: D 542 MET cc_start: 0.8300 (mmp) cc_final: 0.7307 (ptt) REVERT: D 572 LYS cc_start: 0.7451 (tttt) cc_final: 0.7215 (tptt) REVERT: D 680 PHE cc_start: 0.7971 (m-80) cc_final: 0.7530 (m-80) REVERT: D 825 MET cc_start: 0.3225 (mtt) cc_final: 0.2794 (mtt) REVERT: F 120 LYS cc_start: 0.4113 (tttt) cc_final: 0.3806 (mtmt) outliers start: 28 outliers final: 20 residues processed: 236 average time/residue: 0.7775 time to fit residues: 259.7648 Evaluate side-chains 226 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 201 time to evaluate : 2.563 ------------------------------------------------------------------------------- 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 495 TYR Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 648 PHE Chi-restraints excluded: chain B residue 125 HIS Chi-restraints excluded: chain D residue 151 ARG Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 279 ARG Chi-restraints excluded: chain D residue 495 TYR Chi-restraints excluded: chain D residue 497 ASN Chi-restraints excluded: chain D residue 511 TYR Chi-restraints excluded: chain D residue 522 TYR Chi-restraints excluded: chain D residue 653 ASP Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain F residue 233 HIS Chi-restraints excluded: chain F residue 289 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 137 optimal weight: 0.5980 chunk 173 optimal weight: 0.9990 chunk 181 optimal weight: 1.9990 chunk 26 optimal weight: 0.0870 chunk 14 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 chunk 199 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 overall best weight: 1.1364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4703 r_free = 0.4703 target = 0.169457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.137506 restraints weight = 145988.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.139869 restraints weight = 81847.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.140590 restraints weight = 60302.176| |-----------------------------------------------------------------------------| r_work (final): 0.4230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6549 moved from start: 0.7435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17104 Z= 0.112 Angle : 0.502 5.755 23112 Z= 0.261 Chirality : 0.038 0.147 2520 Planarity : 0.004 0.060 3002 Dihedral : 3.921 18.377 2284 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.76 % Allowed : 12.67 % Favored : 85.57 % 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: 1.03 (0.19), residues: 2034 helix: 1.39 (0.17), residues: 988 sheet: -0.56 (0.33), residues: 240 loop : 0.38 (0.23), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 139 HIS 0.002 0.001 HIS B 85 PHE 0.013 0.001 PHE A 482 TYR 0.013 0.001 TYR D 494 ARG 0.008 0.000 ARG A 529 Details of bonding type rmsd hydrogen bonds : bond 0.03477 ( 844) hydrogen bonds : angle 4.79597 ( 2352) metal coordination : bond 0.00679 ( 24) metal coordination : angle 2.00676 ( 30) covalent geometry : bond 0.00249 (17080) covalent geometry : angle 0.49687 (23082) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4068 Ramachandran restraints generated. 2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4068 Ramachandran restraints generated. 2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Residue MET 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Evaluate side-chains 237 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 204 time to evaluate : 2.650 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: A 151 ARG cc_start: 0.7378 (OUTLIER) cc_final: 0.7094 (mmm160) REVERT: A 163 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7883 (tt) REVERT: A 304 MET cc_start: 0.8145 (tpp) cc_final: 0.7812 (tpp) REVERT: A 440 ARG cc_start: 0.3544 (tpm170) cc_final: 0.3204 (tpt170) REVERT: A 476 SER cc_start: 0.8005 (t) cc_final: 0.7691 (m) REVERT: A 495 TYR cc_start: 0.6974 (OUTLIER) cc_final: 0.6163 (t80) REVERT: A 511 TYR cc_start: 0.5335 (OUTLIER) cc_final: 0.2533 (m-80) REVERT: A 542 MET cc_start: 0.6390 (OUTLIER) cc_final: 0.6148 (ptt) REVERT: A 693 MET cc_start: 0.6784 (mmp) cc_final: 0.6510 (mmm) REVERT: A 825 MET cc_start: 0.3070 (mtt) cc_final: 0.2736 (mtt) REVERT: B 109 ARG cc_start: 0.6358 (mpt180) cc_final: 0.5758 (mmt90) REVERT: C 167 GLN cc_start: 0.6948 (pt0) cc_final: 0.6543 (pm20) REVERT: C 243 MET cc_start: 0.8569 (mtp) cc_final: 0.7886 (mpp) REVERT: D 313 MET cc_start: 0.8704 (ttm) cc_final: 0.8428 (ttm) REVERT: D 339 MET cc_start: 0.7411 (mtm) cc_final: 0.7089 (mtt) REVERT: D 488 THR cc_start: 0.8286 (m) cc_final: 0.8032 (p) REVERT: D 495 TYR cc_start: 0.7136 (OUTLIER) cc_final: 0.6502 (t80) REVERT: D 511 TYR cc_start: 0.5417 (OUTLIER) cc_final: 0.3861 (m-80) REVERT: D 542 MET cc_start: 0.8182 (mmp) cc_final: 0.7333 (ptt) REVERT: D 618 VAL cc_start: 0.8366 (t) cc_final: 0.8014 (p) REVERT: D 680 PHE cc_start: 0.7982 (m-80) cc_final: 0.7555 (m-80) REVERT: D 825 MET cc_start: 0.3630 (mtt) cc_final: 0.3166 (mtt) REVERT: E 83 TYR cc_start: 0.7773 (m-80) cc_final: 0.7557 (m-10) REVERT: F 120 LYS cc_start: 0.4140 (tttt) cc_final: 0.3865 (mtmt) outliers start: 33 outliers final: 25 residues processed: 227 average time/residue: 0.7958 time to fit residues: 254.7861 Evaluate side-chains 232 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 200 time to evaluate : 2.623 ------------------------------------------------------------------------------- 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 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 510 LEU Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 648 PHE Chi-restraints excluded: chain B residue 125 HIS Chi-restraints excluded: chain D residue 151 ARG Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 279 ARG Chi-restraints excluded: chain D residue 328 TRP Chi-restraints excluded: chain D residue 495 TYR Chi-restraints excluded: chain D residue 511 TYR Chi-restraints excluded: chain D residue 522 TYR Chi-restraints excluded: chain D residue 525 LEU Chi-restraints excluded: chain D residue 653 ASP Chi-restraints excluded: chain D residue 713 PHE Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain F residue 160 MET Chi-restraints excluded: chain F residue 233 HIS Chi-restraints excluded: chain F residue 289 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 90 optimal weight: 10.0000 chunk 58 optimal weight: 20.0000 chunk 201 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 203 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 188 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 159 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 GLN ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.163109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.130357 restraints weight = 145289.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.130493 restraints weight = 86149.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.132993 restraints weight = 70278.194| |-----------------------------------------------------------------------------| r_work (final): 0.4135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6719 moved from start: 0.8333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 17104 Z= 0.216 Angle : 0.634 9.160 23112 Z= 0.341 Chirality : 0.040 0.159 2520 Planarity : 0.005 0.087 3002 Dihedral : 4.549 22.104 2284 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.82 % Favored : 95.13 % Rotamer: Outliers : 2.18 % Allowed : 13.05 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.10 (0.18), residues: 2034 helix: 0.63 (0.16), residues: 986 sheet: -0.90 (0.32), residues: 240 loop : -0.14 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 139 HIS 0.005 0.001 HIS A 632 PHE 0.017 0.002 PHE D 633 TYR 0.018 0.002 TYR E 86 ARG 0.035 0.001 ARG A 245 Details of bonding type rmsd hydrogen bonds : bond 0.04601 ( 844) hydrogen bonds : angle 5.35558 ( 2352) metal coordination : bond 0.01643 ( 24) metal coordination : angle 3.16669 ( 30) covalent geometry : bond 0.00470 (17080) covalent geometry : angle 0.62378 (23082) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4068 Ramachandran restraints generated. 2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4068 Ramachandran restraints generated. 2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Residue MET 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Evaluate side-chains 248 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 207 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: A 151 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.7168 (mmm160) REVERT: A 304 MET cc_start: 0.7757 (tpp) cc_final: 0.7465 (tpp) REVERT: A 339 MET cc_start: 0.8050 (mtt) cc_final: 0.7839 (mtt) REVERT: A 440 ARG cc_start: 0.3898 (tpm170) cc_final: 0.3639 (tpt170) REVERT: A 476 SER cc_start: 0.8543 (t) cc_final: 0.8342 (m) REVERT: A 495 TYR cc_start: 0.7345 (OUTLIER) cc_final: 0.6452 (t80) REVERT: A 511 TYR cc_start: 0.4738 (OUTLIER) cc_final: 0.2785 (m-80) REVERT: A 825 MET cc_start: 0.3374 (mtt) cc_final: 0.3122 (mtt) REVERT: B 109 ARG cc_start: 0.6692 (mpt180) cc_final: 0.6107 (mmt90) REVERT: C 243 MET cc_start: 0.8630 (mtp) cc_final: 0.8073 (mpp) REVERT: D 429 GLU cc_start: 0.5784 (tm-30) cc_final: 0.5507 (tm-30) REVERT: D 476 SER cc_start: 0.8697 (t) cc_final: 0.8412 (m) REVERT: D 495 TYR cc_start: 0.7278 (OUTLIER) cc_final: 0.6842 (t80) REVERT: D 511 TYR cc_start: 0.5400 (OUTLIER) cc_final: 0.3860 (m-80) REVERT: D 542 MET cc_start: 0.8583 (mmp) cc_final: 0.7256 (ptt) REVERT: D 680 PHE cc_start: 0.7951 (m-80) cc_final: 0.7458 (m-10) REVERT: D 825 MET cc_start: 0.2619 (mtt) cc_final: 0.2162 (mtt) REVERT: E 46 ARG cc_start: 0.7351 (tpp80) cc_final: 0.7021 (ttp-170) REVERT: F 120 LYS cc_start: 0.4550 (tttt) cc_final: 0.4077 (mtmt) outliers start: 41 outliers final: 30 residues processed: 237 average time/residue: 0.7847 time to fit residues: 263.1611 Evaluate side-chains 223 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 188 time to evaluate : 2.644 ------------------------------------------------------------------------------- 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 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 510 LEU Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 648 PHE Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 125 HIS Chi-restraints excluded: chain D residue 151 ARG Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 279 ARG Chi-restraints excluded: chain D residue 328 TRP Chi-restraints excluded: chain D residue 495 TYR Chi-restraints excluded: chain D residue 503 SER Chi-restraints excluded: chain D residue 511 TYR Chi-restraints excluded: chain D residue 522 TYR Chi-restraints excluded: chain D residue 653 ASP Chi-restraints excluded: chain D residue 713 PHE Chi-restraints excluded: chain D residue 861 ARG Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain E residue 120 GLU Chi-restraints excluded: chain F residue 160 MET Chi-restraints excluded: chain F residue 233 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 54 optimal weight: 2.9990 chunk 158 optimal weight: 0.9980 chunk 203 optimal weight: 0.7980 chunk 173 optimal weight: 0.4980 chunk 124 optimal weight: 0.9990 chunk 138 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 196 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 chunk 31 optimal weight: 0.8980 chunk 149 optimal weight: 10.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 167 GLN ** D 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN ** F 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4765 r_free = 0.4765 target = 0.173935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.148369 restraints weight = 160654.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.149911 restraints weight = 132584.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.152122 restraints weight = 88892.251| |-----------------------------------------------------------------------------| r_work (final): 0.4292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6449 moved from start: 0.8405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 17104 Z= 0.109 Angle : 0.540 11.044 23112 Z= 0.277 Chirality : 0.038 0.149 2520 Planarity : 0.004 0.060 3002 Dihedral : 4.070 19.299 2284 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.44 % Allowed : 13.79 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.71 (0.19), residues: 2034 helix: 1.18 (0.16), residues: 986 sheet: -0.76 (0.33), residues: 240 loop : 0.16 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 139 HIS 0.003 0.001 HIS F 214 PHE 0.017 0.001 PHE E 76 TYR 0.012 0.001 TYR F 205 ARG 0.011 0.001 ARG A 245 Details of bonding type rmsd hydrogen bonds : bond 0.03530 ( 844) hydrogen bonds : angle 4.83168 ( 2352) metal coordination : bond 0.00544 ( 24) metal coordination : angle 2.41281 ( 30) covalent geometry : bond 0.00246 (17080) covalent geometry : angle 0.53381 (23082) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4068 Ramachandran restraints generated. 2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4068 Ramachandran restraints generated. 2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Residue MET 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Evaluate side-chains 233 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 206 time to evaluate : 2.628 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 151 ARG cc_start: 0.7653 (OUTLIER) cc_final: 0.7055 (mmm160) REVERT: A 304 MET cc_start: 0.7592 (tpp) cc_final: 0.7357 (tpp) REVERT: A 440 ARG cc_start: 0.3781 (tpm170) cc_final: 0.3568 (tpt170) REVERT: A 495 TYR cc_start: 0.7341 (OUTLIER) cc_final: 0.6472 (t80) REVERT: A 825 MET cc_start: 0.3176 (mtt) cc_final: 0.2913 (mtt) REVERT: B 99 TYR cc_start: 0.6818 (m-80) cc_final: 0.6377 (m-80) REVERT: B 109 ARG cc_start: 0.6580 (mpt180) cc_final: 0.5865 (mmt90) REVERT: C 243 MET cc_start: 0.8401 (mtp) cc_final: 0.7940 (mpp) REVERT: D 339 MET cc_start: 0.7904 (mtm) cc_final: 0.7491 (mtt) REVERT: D 476 SER cc_start: 0.8450 (t) cc_final: 0.8090 (m) REVERT: D 495 TYR cc_start: 0.7110 (OUTLIER) cc_final: 0.6734 (t80) REVERT: D 511 TYR cc_start: 0.5786 (OUTLIER) cc_final: 0.4236 (m-80) REVERT: D 542 MET cc_start: 0.8459 (mmp) cc_final: 0.7348 (ptt) REVERT: D 550 ASP cc_start: 0.6912 (t70) cc_final: 0.6474 (t70) REVERT: D 680 PHE cc_start: 0.7849 (m-80) cc_final: 0.7463 (m-10) REVERT: D 825 MET cc_start: 0.3978 (mtt) cc_final: 0.3473 (mtt) REVERT: E 47 ARG cc_start: 0.7958 (mmt180) cc_final: 0.7005 (mmm160) REVERT: E 48 GLU cc_start: 0.8539 (mt-10) cc_final: 0.8182 (tp30) REVERT: F 120 LYS cc_start: 0.4600 (tttt) cc_final: 0.4228 (mtmt) outliers start: 27 outliers final: 20 residues processed: 225 average time/residue: 0.8158 time to fit residues: 257.0863 Evaluate side-chains 211 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 187 time to evaluate : 2.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 490 ASN Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 648 PHE Chi-restraints excluded: chain B residue 125 HIS Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 279 ARG Chi-restraints excluded: chain D residue 328 TRP Chi-restraints excluded: chain D residue 495 TYR Chi-restraints excluded: chain D residue 511 TYR Chi-restraints excluded: chain D residue 522 TYR Chi-restraints excluded: chain D residue 653 ASP Chi-restraints excluded: chain D residue 713 PHE Chi-restraints excluded: chain D residue 861 ARG Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 103 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 36 optimal weight: 5.9990 chunk 129 optimal weight: 3.9990 chunk 58 optimal weight: 8.9990 chunk 183 optimal weight: 0.9980 chunk 125 optimal weight: 0.0670 chunk 53 optimal weight: 10.0000 chunk 198 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 159 optimal weight: 7.9990 chunk 10 optimal weight: 0.8980 chunk 134 optimal weight: 6.9990 overall best weight: 2.1922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 GLN ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 214 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.163363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.130587 restraints weight = 142975.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.132576 restraints weight = 87559.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.132296 restraints weight = 61044.805| |-----------------------------------------------------------------------------| r_work (final): 0.4117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6758 moved from start: 0.8796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17104 Z= 0.169 Angle : 0.575 8.761 23112 Z= 0.304 Chirality : 0.039 0.150 2520 Planarity : 0.005 0.085 3002 Dihedral : 4.229 20.916 2284 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.49 % Allowed : 14.27 % Favored : 84.24 % 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: 0.46 (0.18), residues: 2034 helix: 0.99 (0.16), residues: 986 sheet: -0.91 (0.32), residues: 240 loop : 0.01 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 791 HIS 0.006 0.001 HIS F 214 PHE 0.017 0.002 PHE E 76 TYR 0.019 0.002 TYR E 83 ARG 0.009 0.001 ARG A 529 Details of bonding type rmsd hydrogen bonds : bond 0.03942 ( 844) hydrogen bonds : angle 5.09626 ( 2352) metal coordination : bond 0.00946 ( 24) metal coordination : angle 2.46332 ( 30) covalent geometry : bond 0.00372 (17080) covalent geometry : angle 0.56854 (23082) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4068 Ramachandran restraints generated. 2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4068 Ramachandran restraints generated. 2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Residue MET 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Evaluate side-chains 218 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 190 time to evaluate : 2.740 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 304 MET cc_start: 0.7646 (tpp) cc_final: 0.7424 (tpp) REVERT: A 440 ARG cc_start: 0.3869 (tpm170) cc_final: 0.3647 (tpt170) REVERT: A 495 TYR cc_start: 0.7311 (OUTLIER) cc_final: 0.6514 (t80) REVERT: A 542 MET cc_start: 0.6993 (ptt) cc_final: 0.6703 (ptt) REVERT: A 573 GLU cc_start: 0.8992 (tt0) cc_final: 0.8014 (tp30) REVERT: A 825 MET cc_start: 0.3327 (mtt) cc_final: 0.3063 (mtt) REVERT: B 109 ARG cc_start: 0.6572 (mpt180) cc_final: 0.6010 (mmt90) REVERT: C 243 MET cc_start: 0.8642 (mtp) cc_final: 0.8074 (mpp) REVERT: D 476 SER cc_start: 0.8603 (t) cc_final: 0.8299 (m) REVERT: D 495 TYR cc_start: 0.7193 (OUTLIER) cc_final: 0.6834 (t80) REVERT: D 511 TYR cc_start: 0.5338 (OUTLIER) cc_final: 0.3595 (m-80) REVERT: D 542 MET cc_start: 0.8733 (mmp) cc_final: 0.7310 (ptt) REVERT: D 550 ASP cc_start: 0.7196 (t70) cc_final: 0.6094 (t70) REVERT: D 618 VAL cc_start: 0.8411 (t) cc_final: 0.8018 (p) REVERT: D 680 PHE cc_start: 0.7960 (m-80) cc_final: 0.7489 (m-10) REVERT: D 825 MET cc_start: 0.3528 (mtt) cc_final: 0.3112 (mtt) REVERT: E 47 ARG cc_start: 0.7935 (mmt180) cc_final: 0.7478 (mmt180) REVERT: E 48 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8256 (tp30) REVERT: F 120 LYS cc_start: 0.4634 (tttt) cc_final: 0.4140 (mtmt) outliers start: 28 outliers final: 21 residues processed: 211 average time/residue: 0.7781 time to fit residues: 232.3959 Evaluate side-chains 205 residues out of total 1884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 181 time to evaluate : 2.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 490 ASN Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 522 TYR Chi-restraints excluded: chain A residue 648 PHE Chi-restraints excluded: chain B residue 125 HIS Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 279 ARG Chi-restraints excluded: chain D residue 328 TRP Chi-restraints excluded: chain D residue 495 TYR Chi-restraints excluded: chain D residue 511 TYR Chi-restraints excluded: chain D residue 522 TYR Chi-restraints excluded: chain D residue 648 PHE Chi-restraints excluded: chain D residue 653 ASP Chi-restraints excluded: chain D residue 713 PHE Chi-restraints excluded: chain D residue 861 ARG Chi-restraints excluded: chain E residue 69 VAL Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 103 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 40 optimal weight: 4.9990 chunk 21 optimal weight: 0.0980 chunk 41 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 85 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 120 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 168 optimal weight: 10.0000 chunk 29 optimal weight: 0.0980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.165120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.132000 restraints weight = 144601.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.134518 restraints weight = 89150.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.135163 restraints weight = 58637.549| |-----------------------------------------------------------------------------| r_work (final): 0.4151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6693 moved from start: 0.8910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17104 Z= 0.118 Angle : 0.535 8.467 23112 Z= 0.276 Chirality : 0.038 0.148 2520 Planarity : 0.005 0.090 3002 Dihedral : 4.029 19.684 2284 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.22 % Allowed : 14.54 % Favored : 84.24 % 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: 0.75 (0.19), residues: 2034 helix: 1.24 (0.16), residues: 984 sheet: -0.79 (0.32), residues: 234 loop : 0.14 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 139 HIS 0.004 0.001 HIS B 85 PHE 0.015 0.001 PHE E 76 TYR 0.016 0.001 TYR B 50 ARG 0.010 0.001 ARG A 245 Details of bonding type rmsd hydrogen bonds : bond 0.03492 ( 844) hydrogen bonds : angle 4.87678 ( 2352) metal coordination : bond 0.00576 ( 24) metal coordination : angle 2.33022 ( 30) covalent geometry : bond 0.00264 (17080) covalent geometry : angle 0.52826 (23082) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9875.56 seconds wall clock time: 171 minutes 10.63 seconds (10270.63 seconds total)