Starting phenix.real_space_refine on Sat Dec 16 00:06:43 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r1g_18810/12_2023/8r1g_18810.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r1g_18810/12_2023/8r1g_18810.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r1g_18810/12_2023/8r1g_18810.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r1g_18810/12_2023/8r1g_18810.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r1g_18810/12_2023/8r1g_18810.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r1g_18810/12_2023/8r1g_18810.pdb" } resolution = 3.99 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.092 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 6 6.06 5 S 112 5.16 5 C 10610 2.51 5 N 2862 2.21 5 O 3142 1.98 5 H 16526 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 33258 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 11110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 681, 11110 Classifications: {'peptide': 681} Link IDs: {'PTRANS': 28, 'TRANS': 652} Chain breaks: 1 Chain: "B" Number of atoms: 2365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 2365 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "C" Number of atoms: 3151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 3151 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 15, 'TRANS': 186} Chain: "D" Number of atoms: 11110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 681, 11110 Classifications: {'peptide': 681} Link IDs: {'PTRANS': 28, 'TRANS': 652} Chain breaks: 1 Chain: "E" Number of atoms: 2365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 2365 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "F" Number of atoms: 3151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 3151 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 15, 'TRANS': 186} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12835 SG CYS B 110 73.866 102.944 46.248 1.00 88.62 S ATOM 12878 SG CYS B 113 74.283 103.712 42.874 1.00 87.95 S ATOM 13405 SG CYS B 143 76.342 100.773 44.385 1.00 87.19 S ATOM 13429 SG CYS B 146 77.307 104.282 45.198 1.00 93.27 S ATOM 11605 SG CYS B 37 66.178 114.896 36.868 1.00114.45 S ATOM 11652 SG CYS B 40 67.616 118.161 36.171 1.00108.22 S ATOM 12158 SG CYS B 70 69.841 114.908 36.696 1.00103.60 S ATOM 12202 SG CYS B 73 68.199 116.574 39.588 1.00 99.17 S ATOM 14814 SG CYS C 176 65.958 71.313 19.330 1.00187.28 S ATOM 15777 SG CYS C 238 64.381 73.597 22.216 1.00182.95 S ATOM 15823 SG CYS C 242 68.011 73.982 21.267 1.00171.60 S ATOM 29461 SG CYS E 110 83.900 48.590 46.629 1.00 65.99 S ATOM 29504 SG CYS E 113 83.446 47.869 43.256 1.00 66.82 S ATOM 30031 SG CYS E 143 81.389 50.778 44.815 1.00 67.41 S ATOM 30055 SG CYS E 146 80.447 47.254 45.593 1.00 72.71 S ATOM 28231 SG CYS E 37 91.546 36.803 37.014 1.00 91.45 S ATOM 28278 SG CYS E 40 90.120 33.544 36.293 1.00 85.52 S ATOM 28784 SG CYS E 70 87.883 36.780 36.885 1.00 82.71 S ATOM 28828 SG CYS E 73 89.563 35.084 39.738 1.00 79.69 S ATOM 31440 SG CYS F 176 91.324 80.561 20.019 1.00183.48 S ATOM 32403 SG CYS F 238 92.967 78.302 22.892 1.00173.40 S ATOM 32449 SG CYS F 242 89.328 77.912 21.982 1.00170.91 S Time building chain proxies: 14.19, per 1000 atoms: 0.43 Number of scatterers: 33258 At special positions: 0 Unit cell: (159.6, 152.88, 122.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 6 29.99 S 112 16.00 O 3142 8.00 N 2862 7.00 C 10610 6.00 H 16526 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 25.53 Conformation dependent library (CDL) restraints added in 3.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 201 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 110 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 143 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 146 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 113 " pdb=" ZN B 202 " pdb="ZN ZN B 202 " - pdb=" SG CYS B 37 " pdb="ZN ZN B 202 " - pdb=" SG CYS B 40 " pdb="ZN ZN B 202 " - pdb=" SG CYS B 73 " pdb="ZN ZN B 202 " - pdb=" SG CYS B 70 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" ND1 HIS C 179 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 238 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 176 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 242 " pdb=" ZN E 201 " pdb="ZN ZN E 201 " - pdb=" SG CYS E 110 " pdb="ZN ZN E 201 " - pdb=" SG CYS E 113 " pdb="ZN ZN E 201 " - pdb=" SG CYS E 143 " pdb="ZN ZN E 201 " - pdb=" SG CYS E 146 " pdb=" ZN E 202 " pdb="ZN ZN E 202 " - pdb=" SG CYS E 37 " pdb="ZN ZN E 202 " - pdb=" SG CYS E 40 " pdb="ZN ZN E 202 " - pdb=" SG CYS E 73 " pdb="ZN ZN E 202 " - pdb=" SG CYS E 70 " pdb=" ZN F 401 " pdb="ZN ZN F 401 " - pdb=" ND1 HIS F 179 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 238 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 176 " pdb="ZN ZN F 401 " - pdb=" SG CYS F 242 " Number of angles added : 30 4068 Ramachandran restraints generated. 2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3904 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 18 sheets defined 56.4% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.08 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: 14.40 Time building geometry restraints manager: 26.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 16490 1.03 - 1.23: 209 1.23 - 1.43: 7003 1.43 - 1.63: 9738 1.63 - 1.82: 166 Bond restraints: 33606 Sorted by residual: bond pdb=" N VAL D 234 " pdb=" H VAL D 234 " ideal model delta sigma weight residual 0.860 0.962 -0.102 2.00e-02 2.50e+03 2.58e+01 bond pdb=" N VAL A 234 " pdb=" H VAL A 234 " ideal model delta sigma weight residual 0.860 0.961 -0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" CB ASN A 258 " pdb=" CG ASN A 258 " ideal model delta sigma weight residual 1.516 1.460 0.056 2.50e-02 1.60e+03 4.93e+00 bond pdb=" CE LYS D 311 " pdb=" NZ LYS D 311 " ideal model delta sigma weight residual 1.489 1.426 0.063 3.00e-02 1.11e+03 4.46e+00 bond pdb=" C ILE A 401 " pdb=" N PRO A 402 " ideal model delta sigma weight residual 1.330 1.354 -0.024 1.25e-02 6.40e+03 3.82e+00 ... (remaining 33601 not shown) Histogram of bond angle deviations from ideal: 99.26 - 106.21: 697 106.21 - 113.17: 38636 113.17 - 120.12: 10980 120.12 - 127.08: 10225 127.08 - 134.03: 150 Bond angle restraints: 60688 Sorted by residual: angle pdb=" CB ARG A 500 " pdb=" CG ARG A 500 " pdb=" CD ARG A 500 " ideal model delta sigma weight residual 111.30 102.62 8.68 2.30e+00 1.89e-01 1.42e+01 angle pdb=" CB ARG D 500 " pdb=" CG ARG D 500 " pdb=" CD ARG D 500 " ideal model delta sigma weight residual 111.30 102.66 8.64 2.30e+00 1.89e-01 1.41e+01 angle pdb=" C GLU A 135 " pdb=" CA GLU A 135 " pdb=" CB GLU A 135 " ideal model delta sigma weight residual 110.46 103.63 6.83 1.94e+00 2.66e-01 1.24e+01 angle pdb=" C GLU D 135 " pdb=" CA GLU D 135 " pdb=" CB GLU D 135 " ideal model delta sigma weight residual 110.46 103.64 6.82 1.94e+00 2.66e-01 1.24e+01 angle pdb=" C PHE D 256 " pdb=" CA PHE D 256 " pdb=" CB PHE D 256 " ideal model delta sigma weight residual 110.88 106.15 4.73 1.57e+00 4.06e-01 9.07e+00 ... (remaining 60683 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.92: 14047 15.92 - 31.85: 878 31.85 - 47.77: 275 47.77 - 63.70: 192 63.70 - 79.62: 70 Dihedral angle restraints: 15462 sinusoidal: 8332 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 15459 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1591 0.053 - 0.107: 635 0.107 - 0.160: 247 0.160 - 0.213: 38 0.213 - 0.267: 9 Chirality restraints: 2520 Sorted by residual: chirality pdb=" CA ASN A 699 " pdb=" N ASN A 699 " pdb=" C ASN A 699 " pdb=" CB ASN A 699 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CA ASN D 699 " pdb=" N ASN D 699 " pdb=" C ASN D 699 " pdb=" CB ASN D 699 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA ARG F 248 " pdb=" N ARG F 248 " pdb=" C ARG F 248 " pdb=" CB ARG F 248 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 2517 not shown) Planarity restraints: 4944 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 500 " 0.754 9.50e-02 1.11e+02 2.52e-01 6.95e+01 pdb=" NE ARG A 500 " -0.024 2.00e-02 2.50e+03 pdb=" CZ ARG A 500 " -0.041 2.00e-02 2.50e+03 pdb=" NH1 ARG A 500 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 500 " 0.008 2.00e-02 2.50e+03 pdb="HH11 ARG A 500 " -0.006 2.00e-02 2.50e+03 pdb="HH12 ARG A 500 " 0.006 2.00e-02 2.50e+03 pdb="HH21 ARG A 500 " 0.004 2.00e-02 2.50e+03 pdb="HH22 ARG A 500 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 500 " -0.754 9.50e-02 1.11e+02 2.52e-01 6.95e+01 pdb=" NE ARG D 500 " 0.024 2.00e-02 2.50e+03 pdb=" CZ ARG D 500 " 0.041 2.00e-02 2.50e+03 pdb=" NH1 ARG D 500 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG D 500 " -0.008 2.00e-02 2.50e+03 pdb="HH11 ARG D 500 " 0.006 2.00e-02 2.50e+03 pdb="HH12 ARG D 500 " -0.006 2.00e-02 2.50e+03 pdb="HH21 ARG D 500 " -0.004 2.00e-02 2.50e+03 pdb="HH22 ARG D 500 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 734 " -0.380 9.50e-02 1.11e+02 1.27e-01 1.73e+01 pdb=" NE ARG A 734 " 0.020 2.00e-02 2.50e+03 pdb=" CZ ARG A 734 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 734 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 734 " -0.004 2.00e-02 2.50e+03 pdb="HH11 ARG A 734 " 0.006 2.00e-02 2.50e+03 pdb="HH12 ARG A 734 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG A 734 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 734 " -0.004 2.00e-02 2.50e+03 ... (remaining 4941 not shown) Histogram of nonbonded interaction distances: 1.22 - 1.90: 179 1.90 - 2.57: 31111 2.57 - 3.25: 104416 3.25 - 3.92: 126028 3.92 - 4.60: 201555 Nonbonded interactions: 463289 Sorted by model distance: nonbonded pdb=" OH TYR A 262 " pdb=" HZ3 LYS D 311 " model vdw 1.223 1.850 nonbonded pdb=" OH TYR A 262 " pdb=" HZ1 LYS D 311 " model vdw 1.543 1.850 nonbonded pdb=" OH TYR A 262 " pdb=" NZ LYS D 311 " model vdw 1.603 2.350 nonbonded pdb=" OE2 GLU A 130 " pdb=" HH TYR A 134 " model vdw 1.680 1.850 nonbonded pdb=" OE2 GLU D 130 " pdb=" HH TYR D 134 " model vdw 1.681 1.850 ... (remaining 463284 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.530 Extract box with map and model: 3.240 Check model and map are aligned: 0.530 Set scattering table: 0.320 Process input model: 110.220 Find NCS groups from input model: 1.470 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5536 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 17080 Z= 0.397 Angle : 0.921 8.676 23082 Z= 0.533 Chirality : 0.065 0.267 2520 Planarity : 0.014 0.326 3002 Dihedral : 11.486 79.623 6542 Min Nonbonded Distance : 1.603 Molprobity Statistics. All-atom Clashscore : 1.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.27 % Allowed : 2.45 % Favored : 97.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.17), residues: 2034 helix: -0.79 (0.15), residues: 964 sheet: -0.26 (0.33), residues: 236 loop : 0.14 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP D 791 HIS 0.011 0.002 HIS F 233 PHE 0.043 0.004 PHE D 256 TYR 0.033 0.004 TYR A 494 ARG 0.028 0.001 ARG D 500 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4068 Ramachandran restraints generated. 2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4068 Ramachandran restraints generated. 2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Residue MET 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Evaluate side-chains 473 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 468 time to evaluate : 2.573 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 outliers start: 5 outliers final: 1 residues processed: 473 average time/residue: 0.8421 time to fit residues: 550.2193 Evaluate side-chains 266 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 265 time to evaluate : 2.615 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3733 time to fit residues: 4.0837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 0.8980 chunk 154 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 159 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 chunk 119 optimal weight: 3.9990 chunk 185 optimal weight: 10.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 D 795 HIS ** E 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN ** E 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 165 GLN F 167 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6120 moved from start: 0.4480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 17080 Z= 0.300 Angle : 0.660 5.563 23082 Z= 0.361 Chirality : 0.041 0.173 2520 Planarity : 0.005 0.051 3002 Dihedral : 4.548 18.349 2284 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.13 % Allowed : 8.63 % Favored : 89.24 % 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: 0.26 (0.18), residues: 2034 helix: 0.49 (0.16), residues: 980 sheet: -0.26 (0.35), residues: 214 loop : 0.12 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 791 HIS 0.007 0.002 HIS B 85 PHE 0.022 0.002 PHE B 52 TYR 0.026 0.002 TYR B 67 ARG 0.006 0.001 ARG B 17 *********************** 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 298 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 258 time to evaluate : 2.846 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 outliers start: 40 outliers final: 25 residues processed: 287 average time/residue: 0.7358 time to fit residues: 306.2494 Evaluate side-chains 237 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 212 time to evaluate : 2.554 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.4028 time to fit residues: 21.5243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 154 optimal weight: 4.9990 chunk 126 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 185 optimal weight: 9.9990 chunk 200 optimal weight: 9.9990 chunk 165 optimal weight: 20.0000 chunk 184 optimal weight: 4.9990 chunk 63 optimal weight: 10.0000 chunk 148 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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** ** C 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 HIS E 98 GLN E 114 GLN F 104 GLN ** F 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6610 moved from start: 0.7062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.095 17080 Z= 0.531 Angle : 0.870 8.497 23082 Z= 0.488 Chirality : 0.047 0.242 2520 Planarity : 0.007 0.087 3002 Dihedral : 5.707 24.343 2284 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 21.14 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.26 % Favored : 94.69 % Rotamer: Outliers : 2.29 % Allowed : 12.94 % 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: -0.97 (0.18), residues: 2034 helix: -0.41 (0.16), residues: 974 sheet: -0.90 (0.34), residues: 212 loop : -0.65 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP C 146 HIS 0.017 0.002 HIS B 85 PHE 0.029 0.004 PHE D 612 TYR 0.028 0.003 TYR B 99 ARG 0.016 0.001 ARG C 290 *********************** 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 273 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 230 time to evaluate : 2.693 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 outliers start: 43 outliers final: 22 residues processed: 260 average time/residue: 0.8622 time to fit residues: 317.6403 Evaluate side-chains 217 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 195 time to evaluate : 2.635 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.5056 time to fit residues: 21.6835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 2.9990 chunk 139 optimal weight: 8.9990 chunk 96 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 chunk 124 optimal weight: 0.9990 chunk 186 optimal weight: 3.9990 chunk 197 optimal weight: 0.0770 chunk 97 optimal weight: 1.9990 chunk 176 optimal weight: 0.9990 chunk 53 optimal weight: 7.9990 overall best weight: 1.4146 ------------------------------------------------------------------------------- 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** ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 GLN ** F 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6464 moved from start: 0.7331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17080 Z= 0.198 Angle : 0.574 7.031 23082 Z= 0.306 Chirality : 0.039 0.146 2520 Planarity : 0.005 0.058 3002 Dihedral : 4.750 21.509 2284 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.01 % Allowed : 14.54 % Favored : 84.45 % 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: -0.07 (0.18), residues: 2034 helix: 0.42 (0.16), residues: 988 sheet: -0.79 (0.35), residues: 216 loop : -0.21 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 139 HIS 0.003 0.001 HIS D 632 PHE 0.018 0.002 PHE B 76 TYR 0.017 0.001 TYR B 50 ARG 0.012 0.001 ARG A 245 *********************** 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 233 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 214 time to evaluate : 2.794 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 outliers start: 19 outliers final: 15 residues processed: 226 average time/residue: 0.8036 time to fit residues: 260.1523 Evaluate side-chains 209 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 194 time to evaluate : 2.739 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 15 outliers final: 1 residues processed: 15 average time/residue: 0.4646 time to fit residues: 14.9872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 9.9990 chunk 111 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 168 optimal weight: 20.0000 chunk 136 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 100 optimal weight: 3.9990 chunk 176 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 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 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6636 moved from start: 0.8347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 17080 Z= 0.336 Angle : 0.661 6.820 23082 Z= 0.364 Chirality : 0.041 0.166 2520 Planarity : 0.005 0.062 3002 Dihedral : 4.952 24.147 2284 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 1.92 % Allowed : 14.80 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.18), residues: 2034 helix: 0.15 (0.16), residues: 988 sheet: -0.95 (0.36), residues: 210 loop : -0.49 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 139 HIS 0.006 0.002 HIS B 133 PHE 0.020 0.002 PHE D 612 TYR 0.023 0.002 TYR E 83 ARG 0.013 0.001 ARG F 156 *********************** 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 242 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 206 time to evaluate : 2.603 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 outliers start: 36 outliers final: 19 residues processed: 229 average time/residue: 0.7627 time to fit residues: 250.2551 Evaluate side-chains 209 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 190 time to evaluate : 2.654 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 19 outliers final: 1 residues processed: 19 average time/residue: 0.3669 time to fit residues: 16.2138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 20.0000 chunk 177 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 chunk 197 optimal weight: 4.9990 chunk 163 optimal weight: 9.9990 chunk 91 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 103 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 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 167 GLN ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6649 moved from start: 0.8850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17080 Z= 0.283 Angle : 0.602 8.197 23082 Z= 0.326 Chirality : 0.040 0.154 2520 Planarity : 0.005 0.050 3002 Dihedral : 4.763 22.965 2284 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.85 % Allowed : 16.61 % Favored : 82.53 % 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: -0.46 (0.18), residues: 2034 helix: 0.18 (0.16), residues: 988 sheet: -1.03 (0.36), residues: 210 loop : -0.53 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 139 HIS 0.005 0.001 HIS E 85 PHE 0.017 0.002 PHE A 612 TYR 0.023 0.002 TYR B 50 ARG 0.007 0.001 ARG E 46 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4068 Ramachandran restraints generated. 2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4068 Ramachandran restraints generated. 2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Residue MET 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Evaluate side-chains 205 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 189 time to evaluate : 2.770 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 outliers start: 16 outliers final: 14 residues processed: 198 average time/residue: 0.7916 time to fit residues: 224.1047 Evaluate side-chains 191 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 177 time to evaluate : 2.513 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 14 outliers final: 1 residues processed: 14 average time/residue: 0.3979 time to fit residues: 13.2983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 chunk 144 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 166 optimal weight: 40.0000 chunk 110 optimal weight: 0.3980 chunk 196 optimal weight: 20.0000 chunk 123 optimal weight: 0.0770 chunk 119 optimal weight: 4.9990 chunk 90 optimal weight: 6.9990 overall best weight: 1.0342 ------------------------------------------------------------------------------- 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 ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6569 moved from start: 0.8928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17080 Z= 0.165 Angle : 0.530 6.978 23082 Z= 0.278 Chirality : 0.038 0.149 2520 Planarity : 0.004 0.049 3002 Dihedral : 4.342 20.573 2284 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.21 % Allowed : 17.09 % Favored : 82.69 % 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: 0.17 (0.19), residues: 2034 helix: 0.71 (0.16), residues: 986 sheet: -0.80 (0.37), residues: 206 loop : -0.20 (0.22), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 139 HIS 0.005 0.001 HIS F 214 PHE 0.017 0.001 PHE A 482 TYR 0.020 0.001 TYR B 50 ARG 0.005 0.000 ARG A 245 *********************** 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 207 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 203 time to evaluate : 2.617 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 outliers start: 4 outliers final: 4 residues processed: 206 average time/residue: 0.8026 time to fit residues: 236.0709 Evaluate side-chains 186 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 182 time to evaluate : 2.594 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.4121 time to fit residues: 6.3031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 117 optimal weight: 0.8980 chunk 59 optimal weight: 30.0000 chunk 38 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 178 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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** ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6559 moved from start: 0.9041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 17080 Z= 0.160 Angle : 0.521 7.177 23082 Z= 0.271 Chirality : 0.038 0.147 2520 Planarity : 0.004 0.047 3002 Dihedral : 4.136 20.190 2284 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.27 % Allowed : 17.25 % Favored : 82.48 % 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: 0.51 (0.19), residues: 2034 helix: 0.99 (0.16), residues: 986 sheet: -0.70 (0.37), residues: 206 loop : -0.02 (0.22), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 139 HIS 0.002 0.000 HIS A 632 PHE 0.017 0.001 PHE D 482 TYR 0.018 0.001 TYR B 50 ARG 0.007 0.000 ARG A 506 *********************** 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 207 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 202 time to evaluate : 2.601 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 outliers start: 5 outliers final: 4 residues processed: 204 average time/residue: 0.7865 time to fit residues: 228.1243 Evaluate side-chains 194 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 190 time to evaluate : 2.691 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.4899 time to fit residues: 6.7044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 4.9990 chunk 171 optimal weight: 1.9990 chunk 183 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 143 optimal weight: 7.9990 chunk 56 optimal weight: 1.9990 chunk 165 optimal weight: 10.0000 chunk 173 optimal weight: 9.9990 chunk 182 optimal weight: 0.7980 chunk 120 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 625 ASN ** A 626 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6616 moved from start: 0.9325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17080 Z= 0.210 Angle : 0.546 9.493 23082 Z= 0.288 Chirality : 0.038 0.150 2520 Planarity : 0.004 0.046 3002 Dihedral : 4.178 20.688 2284 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.37 % Allowed : 17.15 % Favored : 82.48 % 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: 0.47 (0.19), residues: 2034 helix: 0.98 (0.16), residues: 986 sheet: -0.72 (0.37), residues: 206 loop : -0.07 (0.22), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 139 HIS 0.004 0.001 HIS A 632 PHE 0.013 0.001 PHE A 482 TYR 0.023 0.001 TYR B 50 ARG 0.010 0.001 ARG A 506 *********************** 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 201 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 194 time to evaluate : 2.646 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 outliers start: 7 outliers final: 4 residues processed: 198 average time/residue: 0.7931 time to fit residues: 223.9787 Evaluate side-chains 193 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 189 time to evaluate : 2.645 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.3626 time to fit residues: 6.1223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 6.9990 chunk 118 optimal weight: 0.9980 chunk 91 optimal weight: 10.0000 chunk 134 optimal weight: 3.9990 chunk 203 optimal weight: 0.9990 chunk 187 optimal weight: 6.9990 chunk 161 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 125 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 chunk 128 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6581 moved from start: 0.9422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17080 Z= 0.170 Angle : 0.531 8.188 23082 Z= 0.275 Chirality : 0.038 0.147 2520 Planarity : 0.004 0.047 3002 Dihedral : 4.036 19.233 2284 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.16 % Allowed : 17.41 % Favored : 82.43 % 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: 0.68 (0.19), residues: 2034 helix: 1.13 (0.16), residues: 986 sheet: -0.74 (0.37), residues: 210 loop : 0.11 (0.23), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 139 HIS 0.004 0.001 HIS B 31 PHE 0.014 0.001 PHE D 482 TYR 0.021 0.001 TYR B 50 ARG 0.010 0.000 ARG A 710 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4068 Ramachandran restraints generated. 2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4068 Ramachandran restraints generated. 2034 Oldfield, 0 Emsley, 2034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Residue MET 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Evaluate side-chains 201 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 198 time to evaluate : 2.646 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 outliers start: 3 outliers final: 3 residues processed: 199 average time/residue: 0.8295 time to fit residues: 237.3539 Evaluate side-chains 192 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 189 time to evaluate : 2.688 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.5303 time to fit residues: 6.0981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 149 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 162 optimal weight: 30.0000 chunk 67 optimal weight: 20.0000 chunk 166 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 142 optimal weight: 5.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 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 = 0.4622 r_free = 0.4622 target = 0.162903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.129879 restraints weight = 142230.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.131751 restraints weight = 88845.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.132857 restraints weight = 62489.170| |-----------------------------------------------------------------------------| r_work (final): 0.4145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6712 moved from start: 0.9535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17080 Z= 0.165 Angle : 0.521 8.200 23082 Z= 0.269 Chirality : 0.038 0.147 2520 Planarity : 0.004 0.046 3002 Dihedral : 3.938 19.528 2284 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.11 % Allowed : 17.52 % Favored : 82.37 % 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: 0.85 (0.19), residues: 2034 helix: 1.30 (0.17), residues: 986 sheet: -0.68 (0.37), residues: 210 loop : 0.16 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 139 HIS 0.002 0.001 HIS B 85 PHE 0.014 0.001 PHE D 482 TYR 0.022 0.001 TYR B 83 ARG 0.005 0.000 ARG F 282 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6591.28 seconds wall clock time: 118 minutes 31.80 seconds (7111.80 seconds total)