Starting phenix.real_space_refine on Sat Jul 4 15:21:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7cxn_30493/07_2026/7cxn_30493.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cxn_30493/07_2026/7cxn_30493.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7cxn_30493/07_2026/7cxn_30493.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cxn_30493/07_2026/7cxn_30493.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7cxn_30493/07_2026/7cxn_30493.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7cxn_30493/07_2026/7cxn_30493.cif" model { file = "/net/cci-nas-00/data/ceres_data/7cxn_30493/07_2026/7cxn_30493.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cxn_30493/07_2026/7cxn_30493.cif" } resolution = 3.84 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.037 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 8 6.06 5 P 57 5.49 5 S 149 5.16 5 C 13292 2.51 5 N 3614 2.21 5 O 4175 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21295 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 926, 7458 Classifications: {'peptide': 926} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 895} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 1396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1396 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 6, 'TRANS': 180} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'TYR:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "C" Number of atoms: 553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 553 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Chain: "D" Number of atoms: 1414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1414 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 179} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "I" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 545 Classifications: {'RNA': 25} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 16, 'rna3p_pyr': 8} Link IDs: {'rna3p': 24} Chain: "J" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 545 Classifications: {'RNA': 26} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 9, 'rna3p_pyr': 16} Link IDs: {'rna2p': 1, 'rna3p': 24} Chain: "L" Number of atoms: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 128 Classifications: {'RNA': 6} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 1, 'rna3p_pyr': 1} Link IDs: {'rna2p': 3, 'rna3p': 2} Chain: "F" Number of atoms: 4630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4630 Classifications: {'peptide': 596} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 5, 'PTRANS': 30, 'TRANS': 560} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 4618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4618 Classifications: {'peptide': 596} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 4, 'PTRANS': 30, 'TRANS': 561} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 27 Chain: "A" 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: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2446 SG CYS A 301 59.044 66.687 125.669 1.00120.79 S ATOM 2487 SG CYS A 306 58.337 66.866 129.473 1.00109.02 S ATOM 2519 SG CYS A 310 61.753 65.606 128.086 1.00106.10 S ATOM 3927 SG CYS A 487 48.124 78.989 112.682 1.00132.82 S ATOM 5180 SG CYS A 645 47.855 80.227 116.275 1.00129.11 S ATOM 5186 SG CYS A 646 48.897 76.635 115.582 1.00129.46 S ATOM 12066 SG CYS F 5 38.526 77.166 65.507 1.00197.03 S ATOM 12087 SG CYS F 8 39.371 79.862 62.949 1.00196.81 S ATOM 12225 SG CYS F 26 36.565 80.652 64.966 1.00207.13 S ATOM 12246 SG CYS F 29 35.663 78.053 63.206 1.00212.00 S ATOM 12411 SG CYS F 50 23.804 84.901 87.278 1.00252.93 S ATOM 12441 SG CYS F 55 20.831 82.494 87.526 1.00257.68 S ATOM 12574 SG CYS F 72 20.226 85.818 86.079 1.00263.37 S ATOM 12148 SG CYS F 16 31.023 72.587 73.118 1.00204.79 S ATOM 12163 SG CYS F 19 32.116 69.541 71.286 1.00214.40 S ATOM 16696 SG CYS E 5 77.272 115.943 58.881 1.00140.71 S ATOM 16717 SG CYS E 8 79.506 119.058 58.914 1.00146.09 S ATOM 16855 SG CYS E 26 75.589 119.357 59.219 1.00149.43 S ATOM 16876 SG CYS E 29 76.948 118.751 56.213 1.00156.27 S ATOM 17041 SG CYS E 50 49.379 115.931 58.356 1.00185.29 S ATOM 17071 SG CYS E 55 49.243 116.075 54.577 1.00193.67 S ATOM 17204 SG CYS E 72 48.122 119.109 56.517 1.00184.60 S ATOM 16778 SG CYS E 16 68.067 112.253 51.573 1.00144.79 S ATOM 16793 SG CYS E 19 70.696 110.872 49.344 1.00147.10 S Time building chain proxies: 3.79, per 1000 atoms: 0.18 Number of scatterers: 21295 At special positions: 0 Unit cell: (139.4, 159.9, 187.78, 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 8 29.99 S 149 16.00 P 57 15.00 O 4175 8.00 N 3614 7.00 C 13292 6.00 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: 1.51 Conformation dependent library (CDL) restraints added in 692.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " pdb=" ZN E 701 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 29 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 26 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 5 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 8 " pdb=" ZN E 702 " pdb="ZN ZN E 702 " - pdb=" ND1 HIS E 75 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 55 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 72 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 50 " pdb=" ZN E 703 " pdb="ZN ZN E 703 " - pdb=" ND1 HIS E 39 " pdb="ZN ZN E 703 " - pdb=" NE2 HIS E 33 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 16 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 19 " pdb=" ZN F1000 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 26 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 8 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 29 " pdb="ZN ZN F1000 " - pdb=" SG CYS F 5 " pdb=" ZN F1001 " pdb="ZN ZN F1001 " - pdb=" ND1 HIS F 75 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 55 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 72 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 50 " pdb=" ZN F1002 " pdb="ZN ZN F1002 " - pdb=" ND1 HIS F 39 " pdb="ZN ZN F1002 " - pdb=" ND1 HIS F 33 " pdb="ZN ZN F1002 " - pdb=" SG CYS F 16 " pdb="ZN ZN F1002 " - pdb=" SG CYS F 19 " Number of angles added : 28 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4894 Finding SS restraints... Secondary structure from input PDB file: 101 helices and 22 sheets defined 42.8% alpha, 12.5% beta 20 base pairs and 30 stacking pairs defined. Time for finding SS restraints: 2.68 Creating SS restraints... Processing helix chain 'A' and resid 5 through 13 removed outlier: 3.755A pdb=" N ASN A 9 " --> pdb=" O GLN A 5 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLY A 13 " --> pdb=" O ASN A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 63 No H-bonds generated for 'chain 'A' and resid 61 through 63' Processing helix chain 'A' and resid 77 through 91 Processing helix chain 'A' and resid 123 through 133 removed outlier: 3.515A pdb=" N LEU A 127 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 149 removed outlier: 3.505A pdb=" N TYR A 149 " --> pdb=" O ILE A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 158 removed outlier: 3.600A pdb=" N ASN A 158 " --> pdb=" O ASP A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 177 removed outlier: 3.551A pdb=" N VAL A 174 " --> pdb=" O ASP A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 200 removed outlier: 3.523A pdb=" N VAL A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 210 Processing helix chain 'A' and resid 234 through 248 removed outlier: 3.768A pdb=" N TYR A 238 " --> pdb=" O VAL A 234 " (cutoff:3.500A) Proline residue: A 243 - end of helix removed outlier: 4.334A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 255 removed outlier: 3.511A pdb=" N GLU A 254 " --> pdb=" O LEU A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 286 removed outlier: 3.722A pdb=" N ARG A 279 " --> pdb=" O PHE A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 304 through 318 removed outlier: 4.280A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 326 removed outlier: 4.199A pdb=" N PHE A 326 " --> pdb=" O PRO A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 376 Processing helix chain 'A' and resid 377 through 384 removed outlier: 4.185A pdb=" N HIS A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 426 removed outlier: 3.715A pdb=" N TYR A 420 " --> pdb=" O ASN A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 454 Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 468 through 479 removed outlier: 4.415A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 493 Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 511 through 519 removed outlier: 4.163A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 532 Processing helix chain 'A' and resid 561 through 581 removed outlier: 3.577A pdb=" N THR A 565 " --> pdb=" O SER A 561 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA A 581 " --> pdb=" O LYS A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 605 Processing helix chain 'A' and resid 627 through 640 removed outlier: 3.536A pdb=" N ARG A 631 " --> pdb=" O PRO A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 662 removed outlier: 3.836A pdb=" N PHE A 652 " --> pdb=" O LEU A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 709 Processing helix chain 'A' and resid 717 through 733 Processing helix chain 'A' and resid 739 through 752 Processing helix chain 'A' and resid 768 through 773 Processing helix chain 'A' and resid 779 through 791 Processing helix chain 'A' and resid 833 through 842 removed outlier: 3.562A pdb=" N ILE A 837 " --> pdb=" O ASP A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 854 removed outlier: 3.502A pdb=" N LEU A 854 " --> pdb=" O ASP A 851 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 851 through 854' Processing helix chain 'A' and resid 855 through 866 removed outlier: 4.102A pdb=" N PHE A 859 " --> pdb=" O MET A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 872 Processing helix chain 'A' and resid 875 through 903 removed outlier: 3.616A pdb=" N ASP A 879 " --> pdb=" O GLN A 875 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP A 901 " --> pdb=" O GLY A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 916 Processing helix chain 'A' and resid 917 through 923 removed outlier: 4.388A pdb=" N TYR A 921 " --> pdb=" O GLU A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 926 No H-bonds generated for 'chain 'A' and resid 924 through 926' Processing helix chain 'B' and resid 9 through 28 Processing helix chain 'B' and resid 31 through 43 removed outlier: 4.631A pdb=" N SER B 41 " --> pdb=" O LYS B 37 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LEU B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 52 Processing helix chain 'B' and resid 54 through 96 removed outlier: 3.658A pdb=" N GLU B 60 " --> pdb=" O GLN B 56 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS B 61 " --> pdb=" O ARG B 57 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG B 96 " --> pdb=" O PHE B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 109 removed outlier: 3.670A pdb=" N ASN B 104 " --> pdb=" O ASN B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 125 removed outlier: 3.951A pdb=" N LEU B 122 " --> pdb=" O ASN B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 140 Processing helix chain 'C' and resid 3 through 20 Processing helix chain 'C' and resid 21 through 24 Processing helix chain 'C' and resid 25 through 42 Processing helix chain 'C' and resid 45 through 62 removed outlier: 3.948A pdb=" N PHE C 49 " --> pdb=" O THR C 45 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N MET C 62 " --> pdb=" O VAL C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 71 removed outlier: 3.604A pdb=" N LYS C 70 " --> pdb=" O VAL C 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 29 removed outlier: 3.573A pdb=" N ALA D 14 " --> pdb=" O PRO D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 41 Processing helix chain 'D' and resid 42 through 80 removed outlier: 4.766A pdb=" N ASP D 52 " --> pdb=" O GLU D 48 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N MET D 55 " --> pdb=" O ARG D 51 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU D 59 " --> pdb=" O MET D 55 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP D 64 " --> pdb=" O GLU D 60 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLN D 69 " --> pdb=" O GLN D 65 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LYS D 72 " --> pdb=" O THR D 68 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU D 77 " --> pdb=" O GLN D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 99 removed outlier: 6.017A pdb=" N GLN D 88 " --> pdb=" O THR D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 113 removed outlier: 3.557A pdb=" N ILE D 106 " --> pdb=" O ALA D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 140 Processing helix chain 'D' and resid 168 through 172 Processing helix chain 'D' and resid 176 through 180 Processing helix chain 'F' and resid 26 through 37 Processing helix chain 'F' and resid 59 through 61 No H-bonds generated for 'chain 'F' and resid 59 through 61' Processing helix chain 'F' and resid 102 through 112 removed outlier: 3.708A pdb=" N PHE F 106 " --> pdb=" O ASN F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 124 removed outlier: 3.912A pdb=" N TYR F 120 " --> pdb=" O ASN F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 148 Processing helix chain 'F' and resid 259 through 261 No H-bonds generated for 'chain 'F' and resid 259 through 261' Processing helix chain 'F' and resid 262 through 275 removed outlier: 4.250A pdb=" N ASN F 268 " --> pdb=" O SER F 264 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LYS F 271 " --> pdb=" O ALA F 267 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY F 273 " --> pdb=" O TYR F 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 299 removed outlier: 4.363A pdb=" N HIS F 290 " --> pdb=" O THR F 286 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ALA F 292 " --> pdb=" O LYS F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 322 removed outlier: 4.948A pdb=" N LYS F 320 " --> pdb=" O ALA F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 361 through 363 No H-bonds generated for 'chain 'F' and resid 361 through 363' Processing helix chain 'F' and resid 380 through 391 Processing helix chain 'F' and resid 418 through 422 Processing helix chain 'F' and resid 423 through 433 Processing helix chain 'F' and resid 446 through 451 removed outlier: 3.747A pdb=" N THR F 451 " --> pdb=" O GLU F 447 " (cutoff:3.500A) Processing helix chain 'F' and resid 452 through 455 Processing helix chain 'F' and resid 489 through 494 Processing helix chain 'F' and resid 495 through 500 removed outlier: 4.821A pdb=" N GLU F 498 " --> pdb=" O VAL F 495 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU F 500 " --> pdb=" O ARG F 497 " (cutoff:3.500A) Processing helix chain 'F' and resid 515 through 525 removed outlier: 3.526A pdb=" N ALA F 522 " --> pdb=" O GLN F 518 " (cutoff:3.500A) Processing helix chain 'F' and resid 557 through 567 removed outlier: 3.626A pdb=" N ARG F 567 " --> pdb=" O VAL F 563 " (cutoff:3.500A) Processing helix chain 'F' and resid 580 through 584 Processing helix chain 'E' and resid 26 through 36 Processing helix chain 'E' and resid 59 through 62 Processing helix chain 'E' and resid 102 through 112 Processing helix chain 'E' and resid 116 through 124 removed outlier: 3.934A pdb=" N TYR E 120 " --> pdb=" O ASN E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 147 Processing helix chain 'E' and resid 259 through 264 removed outlier: 3.526A pdb=" N PHE E 262 " --> pdb=" O SER E 259 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N SER E 264 " --> pdb=" O GLU E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 275 Processing helix chain 'E' and resid 286 through 299 removed outlier: 4.081A pdb=" N HIS E 290 " --> pdb=" O THR E 286 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ALA E 292 " --> pdb=" O LYS E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 325 removed outlier: 3.765A pdb=" N TYR E 324 " --> pdb=" O LYS E 320 " (cutoff:3.500A) Processing helix chain 'E' and resid 361 through 363 No H-bonds generated for 'chain 'E' and resid 361 through 363' Processing helix chain 'E' and resid 375 through 379 Processing helix chain 'E' and resid 380 through 391 Processing helix chain 'E' and resid 418 through 422 Processing helix chain 'E' and resid 423 through 431 Processing helix chain 'E' and resid 445 through 454 Processing helix chain 'E' and resid 489 through 501 removed outlier: 3.682A pdb=" N ILE E 493 " --> pdb=" O ASN E 489 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL E 495 " --> pdb=" O PRO E 491 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N GLU E 498 " --> pdb=" O GLY E 494 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR E 501 " --> pdb=" O ARG E 497 " (cutoff:3.500A) Processing helix chain 'E' and resid 515 through 525 Processing helix chain 'E' and resid 557 through 566 Processing helix chain 'E' and resid 580 through 584 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 21 removed outlier: 4.963A pdb=" N PHE A 45 " --> pdb=" O ILE A 37 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ILE A 37 " --> pdb=" O PHE A 45 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N LYS A 47 " --> pdb=" O PHE A 35 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N PHE A 35 " --> pdb=" O LYS A 47 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LEU A 49 " --> pdb=" O ARG A 33 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ARG A 33 " --> pdb=" O LEU A 49 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N THR A 51 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N VAL A 31 " --> pdb=" O THR A 51 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N CYS A 53 " --> pdb=" O ASP A 29 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 21 removed outlier: 12.460A pdb=" N LYS A 50 " --> pdb=" O ARG A 74 " (cutoff:3.500A) removed outlier: 11.637A pdb=" N ARG A 74 " --> pdb=" O LYS A 50 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N ASN A 52 " --> pdb=" O VAL A 72 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N VAL A 72 " --> pdb=" O ASN A 52 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N CYS A 54 " --> pdb=" O PHE A 70 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N PHE A 70 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N PHE A 56 " --> pdb=" O SER A 68 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N SER A 68 " --> pdb=" O PHE A 56 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N GLU A 58 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE A 66 " --> pdb=" O GLU A 58 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 201 through 202 Processing sheet with id=AA4, first strand: chain 'A' and resid 352 through 355 removed outlier: 6.706A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 556 through 559 removed outlier: 6.648A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU A 387 " --> pdb=" O MET B 129 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N VAL B 131 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N LEU A 389 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ILE B 185 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N VAL B 159 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N THR B 187 " --> pdb=" O GLN B 157 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LEU B 153 " --> pdb=" O ALA B 191 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 414 through 415 Processing sheet with id=AA7, first strand: chain 'A' and resid 753 through 757 Processing sheet with id=AA8, first strand: chain 'A' and resid 816 through 822 removed outlier: 3.502A pdb=" N ASP A 825 " --> pdb=" O GLN A 822 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 127 through 132 removed outlier: 3.689A pdb=" N THR D 146 " --> pdb=" O ASP D 143 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP D 143 " --> pdb=" O THR D 146 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 3 through 4 Processing sheet with id=AB2, first strand: chain 'F' and resid 70 through 72 Processing sheet with id=AB3, first strand: chain 'F' and resid 152 through 156 removed outlier: 6.994A pdb=" N HIS F 164 " --> pdb=" O ARG F 155 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL F 209 " --> pdb=" O LEU F 163 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N GLY F 184 " --> pdb=" O ILE F 195 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLU F 197 " --> pdb=" O PHE F 182 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N PHE F 182 " --> pdb=" O GLU F 197 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 277 through 278 removed outlier: 6.665A pdb=" N SER F 278 " --> pdb=" O TYR F 398 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE F 304 " --> pdb=" O VAL F 356 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N CYS F 358 " --> pdb=" O ILE F 304 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N TYR F 306 " --> pdb=" O CYS F 358 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 470 through 472 removed outlier: 5.953A pdb=" N ILE F 512 " --> pdb=" O THR F 547 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 470 through 472 removed outlier: 8.360A pdb=" N ASP F 542 " --> pdb=" O VAL F 570 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ILE F 572 " --> pdb=" O ASP F 542 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 3 through 4 removed outlier: 3.602A pdb=" N THR E 12 " --> pdb=" O GLY E 3 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 70 through 71 Processing sheet with id=AB9, first strand: chain 'E' and resid 84 through 85 Processing sheet with id=AC1, first strand: chain 'E' and resid 163 through 167 removed outlier: 7.118A pdb=" N HIS E 164 " --> pdb=" O ARG E 155 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N ASP E 223 " --> pdb=" O VAL E 154 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N PHE E 182 " --> pdb=" O GLU E 197 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLU E 197 " --> pdb=" O PHE E 182 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N GLY E 184 " --> pdb=" O ILE E 195 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 201 through 202 Processing sheet with id=AC3, first strand: chain 'E' and resid 277 through 281 removed outlier: 6.579A pdb=" N SER E 278 " --> pdb=" O TYR E 398 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N GLY E 400 " --> pdb=" O SER E 278 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N LEU E 280 " --> pdb=" O GLY E 400 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE E 399 " --> pdb=" O PHE E 373 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL E 305 " --> pdb=" O VAL E 372 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N CYS E 358 " --> pdb=" O TYR E 306 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA E 308 " --> pdb=" O CYS E 358 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 470 through 471 removed outlier: 6.601A pdb=" N CYS E 471 " --> pdb=" O CYS E 574 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL E 544 " --> pdb=" O LEU E 573 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N ILE E 575 " --> pdb=" O VAL E 544 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N PHE E 546 " --> pdb=" O ILE E 575 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N VAL E 510 " --> pdb=" O ILE E 545 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N THR E 547 " --> pdb=" O VAL E 510 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE E 512 " --> pdb=" O THR E 547 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N PHE E 511 " --> pdb=" O GLN E 531 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 789 hydrogen bonds defined for protein. 2187 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 47 hydrogen bonds 82 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 30 stacking parallelities Total time for adding SS restraints: 4.03 Time building geometry restraints manager: 1.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6508 1.33 - 1.46: 5384 1.46 - 1.58: 9653 1.58 - 1.71: 111 1.71 - 1.83: 210 Bond restraints: 21866 Sorted by residual: bond pdb=" CA LEU A 302 " pdb=" CB LEU A 302 " ideal model delta sigma weight residual 1.531 1.361 0.170 1.57e-02 4.06e+03 1.17e+02 bond pdb=" CA ASP A 303 " pdb=" CB ASP A 303 " ideal model delta sigma weight residual 1.526 1.414 0.113 1.28e-02 6.10e+03 7.75e+01 bond pdb=" CA TRP A 509 " pdb=" C TRP A 509 " ideal model delta sigma weight residual 1.523 1.453 0.070 1.34e-02 5.57e+03 2.73e+01 bond pdb=" N GLY A 510 " pdb=" CA GLY A 510 " ideal model delta sigma weight residual 1.447 1.508 -0.061 1.19e-02 7.06e+03 2.60e+01 bond pdb=" CA LYS A 718 " pdb=" C LYS A 718 " ideal model delta sigma weight residual 1.523 1.461 0.062 1.34e-02 5.57e+03 2.17e+01 ... (remaining 21861 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.90: 29750 4.90 - 9.79: 184 9.79 - 14.69: 33 14.69 - 19.59: 12 19.59 - 24.48: 1 Bond angle restraints: 29980 Sorted by residual: angle pdb=" N ILE E 333 " pdb=" CA ILE E 333 " pdb=" C ILE E 333 " ideal model delta sigma weight residual 111.81 125.42 -13.61 8.60e-01 1.35e+00 2.51e+02 angle pdb=" N ASP A 303 " pdb=" CA ASP A 303 " pdb=" CB ASP A 303 " ideal model delta sigma weight residual 108.96 128.27 -19.31 1.23e+00 6.61e-01 2.46e+02 angle pdb=" N PHE A 275 " pdb=" CA PHE A 275 " pdb=" C PHE A 275 " ideal model delta sigma weight residual 111.54 129.11 -17.57 1.36e+00 5.41e-01 1.67e+02 angle pdb=" N VAL F 348 " pdb=" CA VAL F 348 " pdb=" C VAL F 348 " ideal model delta sigma weight residual 111.58 124.09 -12.51 1.06e+00 8.90e-01 1.39e+02 angle pdb=" N GLN D 157 " pdb=" CA GLN D 157 " pdb=" CB GLN D 157 " ideal model delta sigma weight residual 110.90 95.33 15.57 1.33e+00 5.65e-01 1.37e+02 ... (remaining 29975 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.42: 12513 27.42 - 54.84: 430 54.84 - 82.26: 35 82.26 - 109.68: 5 109.68 - 137.10: 1 Dihedral angle restraints: 12984 sinusoidal: 5398 harmonic: 7586 Sorted by residual: dihedral pdb=" C ASP E 344 " pdb=" N ASP E 344 " pdb=" CA ASP E 344 " pdb=" CB ASP E 344 " ideal model delta harmonic sigma weight residual -122.60 -144.90 22.30 0 2.50e+00 1.60e-01 7.95e+01 dihedral pdb=" N ASP E 344 " pdb=" C ASP E 344 " pdb=" CA ASP E 344 " pdb=" CB ASP E 344 " ideal model delta harmonic sigma weight residual 122.80 143.05 -20.25 0 2.50e+00 1.60e-01 6.56e+01 dihedral pdb=" N ASP A 303 " pdb=" C ASP A 303 " pdb=" CA ASP A 303 " pdb=" CB ASP A 303 " ideal model delta harmonic sigma weight residual 122.80 141.10 -18.30 0 2.50e+00 1.60e-01 5.36e+01 ... (remaining 12981 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.201: 3416 0.201 - 0.403: 36 0.403 - 0.604: 8 0.604 - 0.805: 3 0.805 - 1.006: 2 Chirality restraints: 3465 Sorted by residual: chirality pdb=" CA ASP E 344 " pdb=" N ASP E 344 " pdb=" C ASP E 344 " pdb=" CB ASP E 344 " both_signs ideal model delta sigma weight residual False 2.51 1.50 1.01 2.00e-01 2.50e+01 2.53e+01 chirality pdb=" CA LEU A 302 " pdb=" N LEU A 302 " pdb=" C LEU A 302 " pdb=" CB LEU A 302 " both_signs ideal model delta sigma weight residual False 2.51 1.64 0.87 2.00e-01 2.50e+01 1.88e+01 chirality pdb=" CA ASP A 303 " pdb=" N ASP A 303 " pdb=" C ASP A 303 " pdb=" CB ASP A 303 " both_signs ideal model delta sigma weight residual False 2.51 1.72 0.80 2.00e-01 2.50e+01 1.58e+01 ... (remaining 3462 not shown) Planarity restraints: 3626 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP B 182 " 0.071 5.00e-02 4.00e+02 1.07e-01 1.84e+01 pdb=" N PRO B 183 " -0.185 5.00e-02 4.00e+02 pdb=" CA PRO B 183 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO B 183 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG F 173 " 0.038 5.00e-02 4.00e+02 5.87e-02 5.51e+00 pdb=" N PRO F 174 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO F 174 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO F 174 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 132 " -0.038 5.00e-02 4.00e+02 5.81e-02 5.41e+00 pdb=" N PRO B 133 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO B 133 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 133 " -0.032 5.00e-02 4.00e+02 ... (remaining 3623 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 247 2.42 - 3.04: 15799 3.04 - 3.66: 34744 3.66 - 4.28: 49695 4.28 - 4.90: 75997 Nonbonded interactions: 176482 Sorted by model distance: nonbonded pdb=" CD ARG F 332 " pdb=" O LYS F 347 " model vdw 1.804 3.440 nonbonded pdb=" ND2 ASN F 124 " pdb=" O TYR F 421 " model vdw 1.977 3.120 nonbonded pdb=" OG1 THR E 153 " pdb=" OG SER E 166 " model vdw 2.044 3.040 nonbonded pdb=" O ASP A 846 " pdb=" OG1 THR A 850 " model vdw 2.049 3.040 nonbonded pdb=" O ASP E 260 " pdb=" OG SER E 263 " model vdw 2.087 3.040 ... (remaining 176477 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and ((resid 6 through 8 and (name N or name CA or name C or name O or \ name CB )) or resid 9 through 22 or (resid 23 through 28 and (name N or name CA \ or name C or name O or name CB )) or resid 29 through 191)) selection = (chain 'D' and (resid 6 through 21 or (resid 22 through 28 and (name N or name C \ A or name C or name O or name CB )) or resid 29 through 31 or (resid 32 and (nam \ e N or name CA or name C or name O or name CB )) or resid 33 through 34 or (resi \ d 35 through 37 and (name N or name CA or name C or name O or name CB )) or resi \ d 38 or (resid 39 through 40 and (name N or name CA or name C or name O or name \ CB )) or resid 41 through 42 or (resid 43 and (name N or name CA or name C or na \ me O or name CB )) or resid 44 through 46 or (resid 47 and (name N or name CA or \ name C or name O or name CB )) or resid 48 through 191)) } ncs_group { reference = (chain 'E' and (resid 1 through 226 or (resid 227 and (name N or name CA or name \ C or name O or name CB )) or resid 228 through 703)) selection = (chain 'F' and (resid 1 through 247 or (resid 248 and (name N or name CA or name \ C or name O or name CB )) or resid 249 through 331 or (resid 332 and (name N or \ name CA or name C or name O or name CB )) or resid 333 through 377 or (resid 37 \ 8 through 379 and (name N or name CA or name C or name O or name CB )) or resid \ 380 through 1002)) } 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: 8.640 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: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.070 Set scattering table: 0.030 Process input model: 21.700 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 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 : 0.008 0.170 21898 Z= 0.388 Angle : 1.147 24.482 30008 Z= 0.694 Chirality : 0.067 1.006 3465 Planarity : 0.005 0.107 3626 Dihedral : 13.722 137.102 8090 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 25.83 Ramachandran Plot: Outliers : 0.39 % Allowed : 12.90 % Favored : 86.71 % Rotamer: Outliers : 0.23 % Allowed : 7.44 % Favored : 92.33 % Cbeta Deviations : 0.90 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.37 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.60 (0.13), residues: 2551 helix: -2.69 (0.12), residues: 954 sheet: -2.17 (0.29), residues: 244 loop : -3.60 (0.13), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 409 TYR 0.022 0.002 TYR A 689 PHE 0.016 0.002 PHE A 753 TRP 0.025 0.002 TRP D 182 HIS 0.008 0.001 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00749 / 0.39 (21866) covalent geometry : angle 1.12580 / 0.69 (29980) hydrogen bonds : bond 0.18782 / 12.13 ( 832) hydrogen bonds : angle 8.30496 / 5.89 ( 2269) metal coordination : bond 0.02589 / 1.70 ( 32) metal coordination : angle 7.33295 / 5.40 ( 28) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 174 time to evaluate : 0.687 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: A 242 MET cc_start: 0.9297 (mtt) cc_final: 0.8990 (mtm) REVERT: A 615 MET cc_start: 0.8571 (ptm) cc_final: 0.8248 (ppp) REVERT: A 633 MET cc_start: 0.8974 (tmm) cc_final: 0.8577 (tmm) REVERT: A 668 MET cc_start: 0.9522 (tmm) cc_final: 0.8838 (tmm) REVERT: A 902 MET cc_start: 0.8799 (ttt) cc_final: 0.8586 (ttt) REVERT: B 67 MET cc_start: 0.9415 (ttm) cc_final: 0.9066 (tmm) REVERT: B 142 CYS cc_start: 0.8457 (p) cc_final: 0.8114 (p) REVERT: D 55 MET cc_start: 0.9438 (tmm) cc_final: 0.9034 (tmm) REVERT: D 65 GLN cc_start: 0.9487 (pt0) cc_final: 0.8933 (pp30) REVERT: D 67 MET cc_start: 0.9162 (mtm) cc_final: 0.8812 (mtm) REVERT: D 88 GLN cc_start: 0.9412 (mt0) cc_final: 0.9085 (mp10) REVERT: D 94 MET cc_start: 0.8918 (mtp) cc_final: 0.8577 (ttm) REVERT: D 158 GLN cc_start: 0.8918 (tt0) cc_final: 0.8634 (tm-30) REVERT: F 68 MET cc_start: 0.8931 (pmm) cc_final: 0.8608 (pmm) REVERT: F 378 MET cc_start: 0.8763 (tpp) cc_final: 0.8120 (tpp) REVERT: F 455 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7580 (pp) REVERT: E 363 LEU cc_start: 0.9574 (mt) cc_final: 0.9240 (mt) REVERT: E 561 PHE cc_start: 0.9382 (t80) cc_final: 0.9152 (t80) outliers start: 5 outliers final: 2 residues processed: 179 average time/residue: 0.1607 time to fit residues: 43.0775 Evaluate side-chains 118 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 115 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 383 ASP Chi-restraints excluded: chain F residue 455 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 9.9990 chunk 111 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 88 ASN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 ASN A 492 GLN A 691 ASN A 695 ASN A 789 GLN C 31 GLN D 100 ASN D 108 ASN D 140 ASN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 281 GLN ** F 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 ASN E 281 GLN E 311 HIS E 361 ASN E 518 GLN E 519 ASN E 531 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.052285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.034087 restraints weight = 147666.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.035310 restraints weight = 76351.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 72)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.036067 restraints weight = 49569.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 67)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.036570 restraints weight = 37315.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.036883 restraints weight = 30895.429| |-----------------------------------------------------------------------------| r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 21898 Z= 0.232 Angle : 0.782 15.432 30008 Z= 0.400 Chirality : 0.044 0.265 3465 Planarity : 0.005 0.063 3626 Dihedral : 8.456 132.575 3484 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.07 % Favored : 89.69 % Rotamer: Outliers : 1.50 % Allowed : 13.21 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.37 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.05 (0.15), residues: 2551 helix: -0.91 (0.16), residues: 965 sheet: -1.99 (0.28), residues: 283 loop : -2.99 (0.15), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 96 TYR 0.022 0.002 TYR A 237 PHE 0.025 0.002 PHE B 15 TRP 0.022 0.002 TRP D 182 HIS 0.015 0.001 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.23 (21866) covalent geometry : angle 0.75642 / 0.40 (29980) hydrogen bonds : bond 0.05811 / 3.71 ( 832) hydrogen bonds : angle 5.76334 / 4.07 ( 2269) metal coordination : bond 0.01837 / 1.26 ( 32) metal coordination : angle 6.53326 / 4.85 ( 28) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 134 time to evaluate : 0.618 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: A 615 MET cc_start: 0.8512 (ptm) cc_final: 0.8208 (ppp) REVERT: A 633 MET cc_start: 0.9039 (tmm) cc_final: 0.8728 (tmm) REVERT: A 668 MET cc_start: 0.9488 (tmm) cc_final: 0.8845 (tmm) REVERT: B 49 PHE cc_start: 0.9374 (t80) cc_final: 0.9114 (m-80) REVERT: B 62 MET cc_start: 0.9349 (ppp) cc_final: 0.9035 (ppp) REVERT: B 67 MET cc_start: 0.9423 (ttm) cc_final: 0.9059 (tmm) REVERT: B 94 MET cc_start: 0.9390 (ttm) cc_final: 0.9050 (ttp) REVERT: B 142 CYS cc_start: 0.8742 (p) cc_final: 0.8050 (p) REVERT: C 21 ARG cc_start: 0.8894 (tpp80) cc_final: 0.8687 (tpp80) REVERT: D 55 MET cc_start: 0.9600 (tmm) cc_final: 0.9243 (tmm) REVERT: D 65 GLN cc_start: 0.9411 (pt0) cc_final: 0.8921 (pp30) REVERT: D 67 MET cc_start: 0.9051 (mtm) cc_final: 0.8788 (mtm) REVERT: D 88 GLN cc_start: 0.9357 (mt0) cc_final: 0.9018 (mp10) REVERT: D 90 MET cc_start: 0.9593 (ttp) cc_final: 0.9206 (ttp) REVERT: D 94 MET cc_start: 0.9000 (mtp) cc_final: 0.8770 (mtp) REVERT: F 68 MET cc_start: 0.8962 (pmm) cc_final: 0.8580 (pmm) REVERT: F 159 SER cc_start: 0.8120 (OUTLIER) cc_final: 0.7904 (p) REVERT: F 304 ILE cc_start: 0.9125 (mt) cc_final: 0.8793 (mm) REVERT: F 378 MET cc_start: 0.8860 (tpp) cc_final: 0.8224 (tpp) REVERT: E 363 LEU cc_start: 0.9496 (mt) cc_final: 0.9162 (mt) outliers start: 33 outliers final: 11 residues processed: 161 average time/residue: 0.1381 time to fit residues: 34.5908 Evaluate side-chains 122 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 159 SER Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 455 LEU Chi-restraints excluded: chain F residue 500 LEU Chi-restraints excluded: chain F residue 561 PHE Chi-restraints excluded: chain E residue 464 HIS Chi-restraints excluded: chain E residue 479 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 1 optimal weight: 0.0060 chunk 182 optimal weight: 7.9990 chunk 144 optimal weight: 4.9990 chunk 105 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 94 optimal weight: 20.0000 chunk 155 optimal weight: 6.9990 chunk 135 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 chunk 213 optimal weight: 7.9990 overall best weight: 3.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 695 ASN B 140 ASN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 281 GLN ** F 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 311 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.052288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.034152 restraints weight = 148195.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.035333 restraints weight = 75995.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.036102 restraints weight = 49377.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.036540 restraints weight = 37152.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 72)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.036915 restraints weight = 30982.541| |-----------------------------------------------------------------------------| r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 21898 Z= 0.215 Angle : 0.712 14.394 30008 Z= 0.365 Chirality : 0.042 0.241 3465 Planarity : 0.004 0.060 3626 Dihedral : 8.146 133.907 3481 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.31 % Favored : 89.53 % Rotamer: Outliers : 2.54 % Allowed : 14.16 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.37 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.33 (0.16), residues: 2551 helix: -0.15 (0.16), residues: 955 sheet: -1.89 (0.27), residues: 292 loop : -2.62 (0.16), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 80 TYR 0.020 0.001 TYR A 237 PHE 0.020 0.001 PHE B 15 TRP 0.018 0.001 TRP A 916 HIS 0.013 0.001 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.21 (21866) covalent geometry : angle 0.69045 / 0.36 (29980) hydrogen bonds : bond 0.05073 / 3.26 ( 832) hydrogen bonds : angle 5.27245 / 3.72 ( 2269) metal coordination : bond 0.01794 / 1.21 ( 32) metal coordination : angle 5.67492 / 4.22 ( 28) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 125 time to evaluate : 0.726 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: A 370 GLU cc_start: 0.9177 (OUTLIER) cc_final: 0.8922 (pt0) REVERT: A 615 MET cc_start: 0.8451 (ptm) cc_final: 0.8209 (ppp) REVERT: A 633 MET cc_start: 0.9107 (tmm) cc_final: 0.8771 (tmm) REVERT: A 668 MET cc_start: 0.9456 (tmm) cc_final: 0.8819 (tmm) REVERT: A 902 MET cc_start: 0.8847 (ttt) cc_final: 0.8321 (tmm) REVERT: A 924 MET cc_start: 0.9677 (mmm) cc_final: 0.9249 (mmm) REVERT: B 49 PHE cc_start: 0.9430 (t80) cc_final: 0.9151 (m-80) REVERT: B 94 MET cc_start: 0.9513 (ttm) cc_final: 0.9118 (ttp) REVERT: B 158 GLN cc_start: 0.8988 (tp-100) cc_final: 0.8711 (tp-100) REVERT: D 55 MET cc_start: 0.9596 (tmm) cc_final: 0.9219 (tmm) REVERT: D 65 GLN cc_start: 0.9455 (pt0) cc_final: 0.8958 (pp30) REVERT: D 67 MET cc_start: 0.9018 (mtm) cc_final: 0.8726 (mtm) REVERT: D 70 MET cc_start: 0.9414 (tpp) cc_final: 0.8984 (tmm) REVERT: D 88 GLN cc_start: 0.9359 (mt0) cc_final: 0.9027 (mp10) REVERT: F 68 MET cc_start: 0.8932 (pmm) cc_final: 0.8536 (pmm) REVERT: F 159 SER cc_start: 0.8127 (OUTLIER) cc_final: 0.7914 (p) REVERT: F 281 GLN cc_start: 0.6264 (OUTLIER) cc_final: 0.6033 (pt0) REVERT: F 304 ILE cc_start: 0.9159 (mt) cc_final: 0.8873 (mm) REVERT: F 378 MET cc_start: 0.8870 (tpp) cc_final: 0.8146 (tpp) REVERT: F 576 MET cc_start: 0.6668 (OUTLIER) cc_final: 0.6181 (tmm) REVERT: E 363 LEU cc_start: 0.9514 (mt) cc_final: 0.9139 (mt) REVERT: E 436 MET cc_start: 0.7881 (ptp) cc_final: 0.7430 (ptm) outliers start: 56 outliers final: 25 residues processed: 171 average time/residue: 0.1438 time to fit residues: 38.5283 Evaluate side-chains 142 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 113 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 464 CYS Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain F residue 159 SER Chi-restraints excluded: chain F residue 268 ASN Chi-restraints excluded: chain F residue 281 GLN Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 455 LEU Chi-restraints excluded: chain F residue 500 LEU Chi-restraints excluded: chain F residue 510 VAL Chi-restraints excluded: chain F residue 561 PHE Chi-restraints excluded: chain F residue 576 MET Chi-restraints excluded: chain E residue 68 MET Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 401 ASP Chi-restraints excluded: chain E residue 464 HIS Chi-restraints excluded: chain E residue 479 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 125 optimal weight: 0.9990 chunk 206 optimal weight: 7.9990 chunk 162 optimal weight: 7.9990 chunk 21 optimal weight: 7.9990 chunk 3 optimal weight: 8.9990 chunk 144 optimal weight: 1.9990 chunk 205 optimal weight: 6.9990 chunk 239 optimal weight: 0.4980 chunk 31 optimal weight: 1.9990 chunk 234 optimal weight: 8.9990 chunk 182 optimal weight: 8.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 695 ASN A 822 GLN B 19 GLN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 281 GLN ** F 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 311 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.052673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.034605 restraints weight = 146447.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.035781 restraints weight = 75175.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.036550 restraints weight = 48765.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.037061 restraints weight = 36706.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.037328 restraints weight = 30392.191| |-----------------------------------------------------------------------------| r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 21898 Z= 0.177 Angle : 0.679 14.495 30008 Z= 0.349 Chirality : 0.042 0.240 3465 Planarity : 0.004 0.059 3626 Dihedral : 7.978 132.833 3481 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.74 % Favored : 91.10 % Rotamer: Outliers : 2.41 % Allowed : 15.62 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.37 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.16), residues: 2551 helix: 0.16 (0.17), residues: 958 sheet: -1.57 (0.28), residues: 285 loop : -2.41 (0.16), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 21 TYR 0.017 0.001 TYR A 237 PHE 0.026 0.001 PHE B 15 TRP 0.018 0.001 TRP A 916 HIS 0.012 0.001 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.18 (21866) covalent geometry : angle 0.66208 / 0.35 (29980) hydrogen bonds : bond 0.04744 / 3.05 ( 832) hydrogen bonds : angle 5.00811 / 3.53 ( 2269) metal coordination : bond 0.01533 / 1.03 ( 32) metal coordination : angle 5.03013 / 3.75 ( 28) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 124 time to evaluate : 0.755 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: A 370 GLU cc_start: 0.9155 (OUTLIER) cc_final: 0.8894 (pt0) REVERT: A 380 MET cc_start: 0.9075 (mmt) cc_final: 0.8856 (mmt) REVERT: A 615 MET cc_start: 0.8373 (ptm) cc_final: 0.8083 (tmm) REVERT: A 633 MET cc_start: 0.9066 (tmm) cc_final: 0.8771 (tmm) REVERT: A 668 MET cc_start: 0.9427 (tmm) cc_final: 0.8772 (tmm) REVERT: A 902 MET cc_start: 0.8857 (ttt) cc_final: 0.8375 (tmm) REVERT: B 62 MET cc_start: 0.9345 (ppp) cc_final: 0.9100 (ppp) REVERT: B 94 MET cc_start: 0.9506 (ttm) cc_final: 0.9131 (ttp) REVERT: D 48 GLU cc_start: 0.9140 (pt0) cc_final: 0.8539 (tm-30) REVERT: D 55 MET cc_start: 0.9599 (tmm) cc_final: 0.9219 (tmm) REVERT: D 65 GLN cc_start: 0.9477 (pt0) cc_final: 0.9083 (pp30) REVERT: D 67 MET cc_start: 0.9002 (mtm) cc_final: 0.8706 (mtm) REVERT: D 70 MET cc_start: 0.9406 (tpp) cc_final: 0.8960 (tmm) REVERT: D 88 GLN cc_start: 0.9353 (mt0) cc_final: 0.9033 (mp10) REVERT: F 68 MET cc_start: 0.8889 (pmm) cc_final: 0.8527 (pmm) REVERT: F 295 LEU cc_start: 0.9803 (OUTLIER) cc_final: 0.9572 (mt) REVERT: F 378 MET cc_start: 0.8874 (tpp) cc_final: 0.8144 (tpp) REVERT: F 429 MET cc_start: 0.9175 (tmm) cc_final: 0.8912 (tmm) REVERT: F 576 MET cc_start: 0.6606 (OUTLIER) cc_final: 0.6278 (tmm) REVERT: E 271 LYS cc_start: 0.9432 (OUTLIER) cc_final: 0.8966 (pptt) REVERT: E 363 LEU cc_start: 0.9487 (mt) cc_final: 0.9124 (mt) REVERT: E 436 MET cc_start: 0.7915 (ptp) cc_final: 0.7105 (ptp) outliers start: 53 outliers final: 27 residues processed: 168 average time/residue: 0.1468 time to fit residues: 37.8473 Evaluate side-chains 145 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 114 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 268 ASN Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 332 ARG Chi-restraints excluded: chain F residue 500 LEU Chi-restraints excluded: chain F residue 561 PHE Chi-restraints excluded: chain F residue 576 MET Chi-restraints excluded: chain E residue 68 MET Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 271 LYS Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 401 ASP Chi-restraints excluded: chain E residue 464 HIS Chi-restraints excluded: chain E residue 479 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 153 optimal weight: 6.9990 chunk 200 optimal weight: 3.9990 chunk 116 optimal weight: 0.0050 chunk 93 optimal weight: 9.9990 chunk 255 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 152 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 132 optimal weight: 0.4980 chunk 245 optimal weight: 7.9990 overall best weight: 1.5000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 GLN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 281 GLN F 519 ASN F 557 ASN F 559 ASN E 311 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.053268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.035166 restraints weight = 144439.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.036392 restraints weight = 73456.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.037177 restraints weight = 47578.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.037621 restraints weight = 35861.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.038036 restraints weight = 29806.864| |-----------------------------------------------------------------------------| r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21898 Z= 0.134 Angle : 0.647 14.710 30008 Z= 0.331 Chirality : 0.041 0.235 3465 Planarity : 0.004 0.059 3626 Dihedral : 7.702 131.177 3479 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.27 % Favored : 91.57 % Rotamer: Outliers : 2.13 % Allowed : 16.07 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.37 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.16), residues: 2551 helix: 0.39 (0.17), residues: 960 sheet: -1.16 (0.29), residues: 278 loop : -2.21 (0.16), residues: 1313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 80 TYR 0.014 0.001 TYR A 237 PHE 0.021 0.001 PHE B 15 TRP 0.019 0.001 TRP A 916 HIS 0.010 0.001 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (21866) covalent geometry : angle 0.63364 / 0.33 (29980) hydrogen bonds : bond 0.04505 / 2.91 ( 832) hydrogen bonds : angle 4.74235 / 3.34 ( 2269) metal coordination : bond 0.01253 / 0.84 ( 32) metal coordination : angle 4.32162 / 3.24 ( 28) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 132 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 MET cc_start: 0.9139 (mmm) cc_final: 0.8924 (mmm) REVERT: A 370 GLU cc_start: 0.9153 (OUTLIER) cc_final: 0.8897 (pt0) REVERT: A 377 ASP cc_start: 0.8666 (t0) cc_final: 0.8296 (t0) REVERT: A 615 MET cc_start: 0.8302 (ptm) cc_final: 0.8063 (tmm) REVERT: A 633 MET cc_start: 0.9032 (tmm) cc_final: 0.8624 (tmm) REVERT: A 668 MET cc_start: 0.9385 (tmm) cc_final: 0.8773 (tmm) REVERT: A 855 MET cc_start: 0.8449 (mtm) cc_final: 0.8175 (ptp) REVERT: A 902 MET cc_start: 0.8791 (ttt) cc_final: 0.8384 (tmm) REVERT: A 924 MET cc_start: 0.9679 (mmm) cc_final: 0.9293 (mmm) REVERT: B 49 PHE cc_start: 0.9270 (t80) cc_final: 0.9008 (m-80) REVERT: B 67 MET cc_start: 0.8972 (ppp) cc_final: 0.8732 (tmm) REVERT: B 82 LYS cc_start: 0.9352 (ptpt) cc_final: 0.9094 (ptpp) REVERT: B 94 MET cc_start: 0.9494 (ttm) cc_final: 0.9119 (ttp) REVERT: C 47 GLU cc_start: 0.8805 (tm-30) cc_final: 0.8502 (tm-30) REVERT: C 50 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8451 (mp0) REVERT: D 48 GLU cc_start: 0.9174 (pt0) cc_final: 0.8539 (tm-30) REVERT: D 55 MET cc_start: 0.9592 (tmm) cc_final: 0.9215 (tmm) REVERT: D 65 GLN cc_start: 0.9430 (pt0) cc_final: 0.8996 (pp30) REVERT: D 67 MET cc_start: 0.9000 (mtm) cc_final: 0.8721 (mtm) REVERT: D 70 MET cc_start: 0.9405 (tpp) cc_final: 0.8962 (tmm) REVERT: D 88 GLN cc_start: 0.9356 (mt0) cc_final: 0.9004 (mp10) REVERT: F 68 MET cc_start: 0.8856 (pmm) cc_final: 0.8496 (pmm) REVERT: F 295 LEU cc_start: 0.9801 (OUTLIER) cc_final: 0.9531 (mt) REVERT: F 304 ILE cc_start: 0.9177 (mt) cc_final: 0.8818 (mm) REVERT: F 378 MET cc_start: 0.8867 (tpp) cc_final: 0.8141 (tpp) REVERT: F 429 MET cc_start: 0.9167 (tmm) cc_final: 0.8941 (tmm) REVERT: F 576 MET cc_start: 0.6550 (OUTLIER) cc_final: 0.6264 (tmm) REVERT: E 363 LEU cc_start: 0.9476 (mt) cc_final: 0.9099 (mt) REVERT: E 436 MET cc_start: 0.7911 (ptp) cc_final: 0.7614 (ptp) REVERT: E 474 MET cc_start: 0.7787 (tpt) cc_final: 0.7227 (tpt) outliers start: 47 outliers final: 24 residues processed: 170 average time/residue: 0.1346 time to fit residues: 35.8356 Evaluate side-chains 143 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 116 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 262 PHE Chi-restraints excluded: chain F residue 268 ASN Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 332 ARG Chi-restraints excluded: chain F residue 404 GLN Chi-restraints excluded: chain F residue 500 LEU Chi-restraints excluded: chain F residue 561 PHE Chi-restraints excluded: chain F residue 576 MET Chi-restraints excluded: chain E residue 68 MET Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 401 ASP Chi-restraints excluded: chain E residue 479 VAL Chi-restraints excluded: chain E residue 531 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 234 optimal weight: 7.9990 chunk 197 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 254 optimal weight: 0.7980 chunk 130 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 chunk 202 optimal weight: 10.0000 chunk 124 optimal weight: 8.9990 chunk 217 optimal weight: 8.9990 chunk 147 optimal weight: 3.9990 chunk 250 optimal weight: 7.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 ASN B 140 ASN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 311 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.053333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.035260 restraints weight = 145059.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.036423 restraints weight = 73498.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.037209 restraints weight = 47452.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 68)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.037743 restraints weight = 35492.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.038051 restraints weight = 29292.451| |-----------------------------------------------------------------------------| r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21898 Z= 0.142 Angle : 0.650 14.725 30008 Z= 0.331 Chirality : 0.041 0.234 3465 Planarity : 0.004 0.057 3626 Dihedral : 7.617 131.370 3479 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.84 % Favored : 92.00 % Rotamer: Outliers : 2.72 % Allowed : 16.57 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.37 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.16), residues: 2551 helix: 0.47 (0.17), residues: 960 sheet: -1.01 (0.29), residues: 288 loop : -2.13 (0.16), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 80 TYR 0.014 0.001 TYR A 237 PHE 0.018 0.001 PHE D 92 TRP 0.017 0.001 TRP A 916 HIS 0.010 0.001 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (21866) covalent geometry : angle 0.63771 / 0.33 (29980) hydrogen bonds : bond 0.04388 / 2.82 ( 832) hydrogen bonds : angle 4.67301 / 3.29 ( 2269) metal coordination : bond 0.01272 / 0.86 ( 32) metal coordination : angle 4.10233 / 3.06 ( 28) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 127 time to evaluate : 0.790 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: A 370 GLU cc_start: 0.9163 (OUTLIER) cc_final: 0.8906 (pt0) REVERT: A 377 ASP cc_start: 0.8663 (t0) cc_final: 0.8297 (t0) REVERT: A 633 MET cc_start: 0.9110 (tmm) cc_final: 0.8677 (tmm) REVERT: A 668 MET cc_start: 0.9366 (tmm) cc_final: 0.8725 (tmm) REVERT: A 855 MET cc_start: 0.8609 (mtm) cc_final: 0.8240 (ptp) REVERT: A 902 MET cc_start: 0.8906 (ttt) cc_final: 0.8281 (tmm) REVERT: A 924 MET cc_start: 0.9687 (mmm) cc_final: 0.9196 (mmm) REVERT: B 49 PHE cc_start: 0.9253 (t80) cc_final: 0.8999 (m-80) REVERT: B 67 MET cc_start: 0.9012 (ppp) cc_final: 0.8777 (tmm) REVERT: B 82 LYS cc_start: 0.9351 (ptpt) cc_final: 0.9131 (pttm) REVERT: B 94 MET cc_start: 0.9468 (ttm) cc_final: 0.9122 (ttp) REVERT: C 70 LYS cc_start: 0.9555 (mtpp) cc_final: 0.9345 (mtmm) REVERT: D 48 GLU cc_start: 0.9171 (pt0) cc_final: 0.8551 (tm-30) REVERT: D 55 MET cc_start: 0.9614 (tmm) cc_final: 0.9233 (tmm) REVERT: D 65 GLN cc_start: 0.9451 (pt0) cc_final: 0.9042 (pp30) REVERT: D 67 MET cc_start: 0.9079 (mtm) cc_final: 0.8710 (mtm) REVERT: D 70 MET cc_start: 0.9441 (tpp) cc_final: 0.8998 (tmm) REVERT: D 88 GLN cc_start: 0.9451 (mt0) cc_final: 0.9071 (mp10) REVERT: D 90 MET cc_start: 0.9556 (ttp) cc_final: 0.9133 (tmm) REVERT: F 68 MET cc_start: 0.8864 (pmm) cc_final: 0.8471 (pmm) REVERT: F 295 LEU cc_start: 0.9803 (OUTLIER) cc_final: 0.9519 (mt) REVERT: F 304 ILE cc_start: 0.9157 (mt) cc_final: 0.8791 (mm) REVERT: F 378 MET cc_start: 0.8869 (tpp) cc_final: 0.8137 (tpp) REVERT: F 429 MET cc_start: 0.9176 (tmm) cc_final: 0.8953 (tmm) REVERT: F 576 MET cc_start: 0.6669 (OUTLIER) cc_final: 0.6339 (tmm) REVERT: E 363 LEU cc_start: 0.9493 (mt) cc_final: 0.9111 (mt) REVERT: E 436 MET cc_start: 0.8005 (ptp) cc_final: 0.7607 (ptp) REVERT: E 474 MET cc_start: 0.7616 (tpt) cc_final: 0.7048 (tpt) outliers start: 60 outliers final: 39 residues processed: 178 average time/residue: 0.1559 time to fit residues: 43.7373 Evaluate side-chains 161 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 119 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 262 PHE Chi-restraints excluded: chain F residue 268 ASN Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 332 ARG Chi-restraints excluded: chain F residue 404 GLN Chi-restraints excluded: chain F residue 444 CYS Chi-restraints excluded: chain F residue 500 LEU Chi-restraints excluded: chain F residue 510 VAL Chi-restraints excluded: chain F residue 561 PHE Chi-restraints excluded: chain F residue 576 MET Chi-restraints excluded: chain E residue 68 MET Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 464 HIS Chi-restraints excluded: chain E residue 479 VAL Chi-restraints excluded: chain E residue 531 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 8 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 158 optimal weight: 10.0000 chunk 211 optimal weight: 6.9990 chunk 194 optimal weight: 9.9990 chunk 24 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 chunk 227 optimal weight: 8.9990 chunk 3 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 311 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.053011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.035021 restraints weight = 144986.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.036177 restraints weight = 73552.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.036970 restraints weight = 47576.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.037477 restraints weight = 35763.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.037789 restraints weight = 29531.541| |-----------------------------------------------------------------------------| r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21898 Z= 0.158 Angle : 0.655 14.729 30008 Z= 0.332 Chirality : 0.041 0.235 3465 Planarity : 0.004 0.057 3626 Dihedral : 7.613 131.792 3479 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.51 % Favored : 91.42 % Rotamer: Outliers : 2.77 % Allowed : 16.93 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.37 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.16), residues: 2551 helix: 0.50 (0.17), residues: 969 sheet: -1.03 (0.30), residues: 280 loop : -2.07 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 80 TYR 0.017 0.001 TYR A 237 PHE 0.018 0.001 PHE B 15 TRP 0.016 0.001 TRP A 916 HIS 0.006 0.001 HIS A 892 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.16 (21866) covalent geometry : angle 0.64364 / 0.33 (29980) hydrogen bonds : bond 0.04335 / 2.80 ( 832) hydrogen bonds : angle 4.62874 / 3.25 ( 2269) metal coordination : bond 0.01371 / 0.91 ( 32) metal coordination : angle 4.08928 / 3.03 ( 28) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 121 time to evaluate : 0.743 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: A 370 GLU cc_start: 0.9160 (OUTLIER) cc_final: 0.8908 (pt0) REVERT: A 377 ASP cc_start: 0.8679 (t0) cc_final: 0.8345 (t0) REVERT: A 380 MET cc_start: 0.9265 (mmt) cc_final: 0.8994 (mmt) REVERT: A 615 MET cc_start: 0.8384 (ptm) cc_final: 0.8095 (tmm) REVERT: A 633 MET cc_start: 0.9107 (tmm) cc_final: 0.8652 (tmm) REVERT: A 668 MET cc_start: 0.9375 (tmm) cc_final: 0.8714 (tmm) REVERT: A 855 MET cc_start: 0.8607 (mtm) cc_final: 0.8247 (ptp) REVERT: A 902 MET cc_start: 0.8873 (ttt) cc_final: 0.8309 (tmm) REVERT: A 924 MET cc_start: 0.9684 (mmm) cc_final: 0.9148 (mmm) REVERT: B 49 PHE cc_start: 0.9236 (t80) cc_final: 0.8983 (m-80) REVERT: B 62 MET cc_start: 0.9364 (ppp) cc_final: 0.8982 (ppp) REVERT: B 67 MET cc_start: 0.9020 (ppp) cc_final: 0.8777 (tmm) REVERT: B 82 LYS cc_start: 0.9368 (ptpt) cc_final: 0.9102 (ptpp) REVERT: B 94 MET cc_start: 0.9474 (ttm) cc_final: 0.9099 (ttp) REVERT: D 48 GLU cc_start: 0.9176 (pt0) cc_final: 0.8520 (tm-30) REVERT: D 55 MET cc_start: 0.9610 (tmm) cc_final: 0.9225 (tmm) REVERT: D 65 GLN cc_start: 0.9453 (pt0) cc_final: 0.9058 (pp30) REVERT: D 67 MET cc_start: 0.9088 (mtm) cc_final: 0.8730 (mtm) REVERT: D 70 MET cc_start: 0.9443 (tpp) cc_final: 0.8994 (tmm) REVERT: D 88 GLN cc_start: 0.9456 (mt0) cc_final: 0.9056 (mp10) REVERT: D 90 MET cc_start: 0.9573 (ttp) cc_final: 0.9155 (tmm) REVERT: F 68 MET cc_start: 0.8846 (pmm) cc_final: 0.8473 (pmm) REVERT: F 295 LEU cc_start: 0.9803 (OUTLIER) cc_final: 0.9525 (mt) REVERT: F 304 ILE cc_start: 0.9175 (mt) cc_final: 0.8833 (mm) REVERT: F 378 MET cc_start: 0.8880 (tpp) cc_final: 0.8166 (tpp) REVERT: F 429 MET cc_start: 0.9178 (tmm) cc_final: 0.8936 (tmm) REVERT: F 576 MET cc_start: 0.6810 (OUTLIER) cc_final: 0.6492 (tmm) REVERT: E 68 MET cc_start: 0.1674 (OUTLIER) cc_final: 0.1423 (tpt) REVERT: E 363 LEU cc_start: 0.9504 (mt) cc_final: 0.9114 (mt) REVERT: E 436 MET cc_start: 0.7998 (ptp) cc_final: 0.7636 (ptp) REVERT: E 474 MET cc_start: 0.7647 (tpt) cc_final: 0.7059 (tpt) REVERT: E 561 PHE cc_start: 0.9429 (t80) cc_final: 0.9177 (t80) outliers start: 61 outliers final: 41 residues processed: 171 average time/residue: 0.1326 time to fit residues: 35.4826 Evaluate side-chains 159 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 114 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 262 PHE Chi-restraints excluded: chain F residue 268 ASN Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 332 ARG Chi-restraints excluded: chain F residue 398 TYR Chi-restraints excluded: chain F residue 404 GLN Chi-restraints excluded: chain F residue 444 CYS Chi-restraints excluded: chain F residue 500 LEU Chi-restraints excluded: chain F residue 510 VAL Chi-restraints excluded: chain F residue 561 PHE Chi-restraints excluded: chain F residue 576 MET Chi-restraints excluded: chain E residue 68 MET Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 318 CYS Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 401 ASP Chi-restraints excluded: chain E residue 464 HIS Chi-restraints excluded: chain E residue 479 VAL Chi-restraints excluded: chain E residue 531 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 140 optimal weight: 10.0000 chunk 94 optimal weight: 6.9990 chunk 120 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 101 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 171 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 537 GLN E 311 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.053928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.035783 restraints weight = 143839.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.037003 restraints weight = 73616.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.037823 restraints weight = 47668.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.038344 restraints weight = 35545.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.038635 restraints weight = 29378.100| |-----------------------------------------------------------------------------| r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21898 Z= 0.116 Angle : 0.633 14.880 30008 Z= 0.320 Chirality : 0.040 0.228 3465 Planarity : 0.004 0.057 3626 Dihedral : 7.479 129.243 3479 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.98 % Favored : 92.94 % Rotamer: Outliers : 2.09 % Allowed : 17.88 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.37 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.17), residues: 2551 helix: 0.60 (0.17), residues: 965 sheet: -0.82 (0.30), residues: 269 loop : -1.93 (0.17), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 80 TYR 0.011 0.001 TYR A 237 PHE 0.017 0.001 PHE B 15 TRP 0.019 0.001 TRP B 182 HIS 0.006 0.001 HIS A 892 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (21866) covalent geometry : angle 0.62347 / 0.32 (29980) hydrogen bonds : bond 0.04250 / 2.74 ( 832) hydrogen bonds : angle 4.46409 / 3.13 ( 2269) metal coordination : bond 0.01130 / 0.75 ( 32) metal coordination : angle 3.55908 / 2.65 ( 28) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 127 time to evaluate : 0.700 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: A 370 GLU cc_start: 0.9161 (OUTLIER) cc_final: 0.8915 (pt0) REVERT: A 377 ASP cc_start: 0.8643 (t0) cc_final: 0.8287 (t0) REVERT: A 615 MET cc_start: 0.8186 (ptm) cc_final: 0.7911 (tmm) REVERT: A 633 MET cc_start: 0.9017 (tmm) cc_final: 0.8625 (tmm) REVERT: A 668 MET cc_start: 0.9325 (tmm) cc_final: 0.8716 (tmm) REVERT: A 855 MET cc_start: 0.8511 (mtm) cc_final: 0.8189 (ptp) REVERT: A 902 MET cc_start: 0.8787 (ttt) cc_final: 0.8274 (tmm) REVERT: A 924 MET cc_start: 0.9673 (mmm) cc_final: 0.9102 (mmm) REVERT: B 49 PHE cc_start: 0.9231 (t80) cc_final: 0.8988 (m-80) REVERT: B 62 MET cc_start: 0.9223 (ppp) cc_final: 0.8924 (ppp) REVERT: B 67 MET cc_start: 0.9069 (ppp) cc_final: 0.8862 (tmm) REVERT: B 82 LYS cc_start: 0.9357 (ptpt) cc_final: 0.9115 (ptpp) REVERT: C 70 LYS cc_start: 0.9611 (mtpp) cc_final: 0.9288 (mtmm) REVERT: D 48 GLU cc_start: 0.9206 (pt0) cc_final: 0.8591 (tm-30) REVERT: D 55 MET cc_start: 0.9605 (tmm) cc_final: 0.9228 (tmm) REVERT: D 65 GLN cc_start: 0.9398 (pt0) cc_final: 0.9029 (pp30) REVERT: D 67 MET cc_start: 0.9070 (mtm) cc_final: 0.8620 (mtm) REVERT: D 70 MET cc_start: 0.9424 (tpp) cc_final: 0.8973 (tmm) REVERT: D 88 GLN cc_start: 0.9457 (mt0) cc_final: 0.9147 (mp10) REVERT: D 90 MET cc_start: 0.9557 (ttp) cc_final: 0.9201 (tmm) REVERT: F 68 MET cc_start: 0.8809 (pmm) cc_final: 0.8456 (pmm) REVERT: F 295 LEU cc_start: 0.9803 (OUTLIER) cc_final: 0.9517 (mt) REVERT: F 304 ILE cc_start: 0.9163 (mt) cc_final: 0.8820 (mm) REVERT: F 378 MET cc_start: 0.8902 (tpp) cc_final: 0.8377 (tpp) REVERT: F 429 MET cc_start: 0.9162 (tmm) cc_final: 0.8938 (tmm) REVERT: F 576 MET cc_start: 0.6747 (OUTLIER) cc_final: 0.6273 (tmm) REVERT: E 68 MET cc_start: 0.2227 (tpt) cc_final: 0.2000 (tpt) REVERT: E 363 LEU cc_start: 0.9482 (mt) cc_final: 0.9091 (mt) REVERT: E 436 MET cc_start: 0.7941 (ptp) cc_final: 0.7618 (ptp) REVERT: E 474 MET cc_start: 0.7299 (tpt) cc_final: 0.6732 (tpt) outliers start: 46 outliers final: 31 residues processed: 165 average time/residue: 0.1362 time to fit residues: 35.2085 Evaluate side-chains 155 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 121 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 262 PHE Chi-restraints excluded: chain F residue 268 ASN Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 332 ARG Chi-restraints excluded: chain F residue 404 GLN Chi-restraints excluded: chain F residue 444 CYS Chi-restraints excluded: chain F residue 500 LEU Chi-restraints excluded: chain F residue 510 VAL Chi-restraints excluded: chain F residue 576 MET Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 464 HIS Chi-restraints excluded: chain E residue 479 VAL Chi-restraints excluded: chain E residue 531 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 77 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 135 optimal weight: 10.0000 chunk 152 optimal weight: 6.9990 chunk 247 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 144 optimal weight: 7.9990 chunk 68 optimal weight: 7.9990 chunk 121 optimal weight: 10.0000 chunk 138 optimal weight: 10.0000 chunk 186 optimal weight: 6.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 79 ASN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 695 ASN A 886 GLN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 311 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.052791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.034887 restraints weight = 143911.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.036044 restraints weight = 73672.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.036829 restraints weight = 47798.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.037323 restraints weight = 35879.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.037657 restraints weight = 29688.353| |-----------------------------------------------------------------------------| r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21898 Z= 0.186 Angle : 0.675 14.851 30008 Z= 0.340 Chirality : 0.041 0.233 3465 Planarity : 0.004 0.055 3626 Dihedral : 7.548 132.313 3479 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.62 % Favored : 91.30 % Rotamer: Outliers : 2.13 % Allowed : 18.29 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.37 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.17), residues: 2551 helix: 0.55 (0.17), residues: 972 sheet: -0.99 (0.31), residues: 258 loop : -1.90 (0.17), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 80 TYR 0.018 0.001 TYR A 237 PHE 0.018 0.001 PHE E 561 TRP 0.014 0.001 TRP A 916 HIS 0.006 0.001 HIS A 892 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.19 (21866) covalent geometry : angle 0.66374 / 0.34 (29980) hydrogen bonds : bond 0.04253 / 2.75 ( 832) hydrogen bonds : angle 4.59651 / 3.23 ( 2269) metal coordination : bond 0.01513 / 0.98 ( 32) metal coordination : angle 3.99847 / 2.95 ( 28) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 122 time to evaluate : 0.649 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: A 370 GLU cc_start: 0.9147 (OUTLIER) cc_final: 0.8890 (pt0) REVERT: A 377 ASP cc_start: 0.8610 (t0) cc_final: 0.8286 (t0) REVERT: A 519 MET cc_start: 0.9062 (ttm) cc_final: 0.8860 (ttm) REVERT: A 566 MET cc_start: 0.9202 (tpp) cc_final: 0.8861 (mmm) REVERT: A 615 MET cc_start: 0.8332 (ptm) cc_final: 0.8112 (tmm) REVERT: A 633 MET cc_start: 0.9083 (tmm) cc_final: 0.8758 (tmm) REVERT: A 668 MET cc_start: 0.9328 (tmm) cc_final: 0.8675 (tmm) REVERT: A 855 MET cc_start: 0.8504 (mtm) cc_final: 0.8303 (ptp) REVERT: A 902 MET cc_start: 0.8799 (ttt) cc_final: 0.8341 (tmm) REVERT: A 924 MET cc_start: 0.9683 (mmm) cc_final: 0.9103 (mmm) REVERT: B 49 PHE cc_start: 0.9214 (t80) cc_final: 0.8955 (m-80) REVERT: B 62 MET cc_start: 0.9237 (ppp) cc_final: 0.8877 (ppp) REVERT: B 67 MET cc_start: 0.9063 (ppp) cc_final: 0.8848 (tmm) REVERT: B 82 LYS cc_start: 0.9369 (ptpt) cc_final: 0.9132 (pttm) REVERT: B 94 MET cc_start: 0.8520 (ttt) cc_final: 0.8233 (tmm) REVERT: C 70 LYS cc_start: 0.9595 (mtpp) cc_final: 0.9299 (mtmm) REVERT: D 55 MET cc_start: 0.9591 (tmm) cc_final: 0.9201 (tmm) REVERT: D 65 GLN cc_start: 0.9397 (pt0) cc_final: 0.9036 (pp30) REVERT: D 67 MET cc_start: 0.9080 (mtm) cc_final: 0.8740 (mtm) REVERT: D 70 MET cc_start: 0.9432 (tpp) cc_final: 0.8986 (tmm) REVERT: D 88 GLN cc_start: 0.9462 (mt0) cc_final: 0.9061 (mp10) REVERT: D 90 MET cc_start: 0.9559 (ttp) cc_final: 0.9257 (tmm) REVERT: F 68 MET cc_start: 0.8783 (pmm) cc_final: 0.8452 (pmm) REVERT: F 178 ARG cc_start: 0.7732 (mmm160) cc_final: 0.5920 (mtp85) REVERT: F 295 LEU cc_start: 0.9808 (OUTLIER) cc_final: 0.9527 (mt) REVERT: F 304 ILE cc_start: 0.9205 (mt) cc_final: 0.8867 (mm) REVERT: F 378 MET cc_start: 0.8875 (tpp) cc_final: 0.8173 (tpp) REVERT: F 576 MET cc_start: 0.6865 (OUTLIER) cc_final: 0.6404 (tmm) REVERT: E 68 MET cc_start: 0.1817 (OUTLIER) cc_final: 0.1611 (tpt) REVERT: E 164 HIS cc_start: 0.9107 (OUTLIER) cc_final: 0.8805 (m-70) REVERT: E 363 LEU cc_start: 0.9548 (mt) cc_final: 0.9140 (mt) REVERT: E 436 MET cc_start: 0.7928 (ptp) cc_final: 0.7599 (ptp) REVERT: E 474 MET cc_start: 0.7419 (tpt) cc_final: 0.6823 (tpt) outliers start: 47 outliers final: 36 residues processed: 158 average time/residue: 0.1498 time to fit residues: 36.4203 Evaluate side-chains 158 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 117 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 268 ASN Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 332 ARG Chi-restraints excluded: chain F residue 398 TYR Chi-restraints excluded: chain F residue 404 GLN Chi-restraints excluded: chain F residue 436 MET Chi-restraints excluded: chain F residue 444 CYS Chi-restraints excluded: chain F residue 500 LEU Chi-restraints excluded: chain F residue 510 VAL Chi-restraints excluded: chain F residue 561 PHE Chi-restraints excluded: chain F residue 576 MET Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 68 MET Chi-restraints excluded: chain E residue 164 HIS Chi-restraints excluded: chain E residue 318 CYS Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 464 HIS Chi-restraints excluded: chain E residue 479 VAL Chi-restraints excluded: chain E residue 531 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 247 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 181 optimal weight: 6.9990 chunk 79 optimal weight: 0.5980 chunk 162 optimal weight: 3.9990 chunk 26 optimal weight: 0.4980 chunk 211 optimal weight: 1.9990 chunk 246 optimal weight: 0.8980 chunk 206 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 173 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 GLN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 GLN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 531 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.053799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.035765 restraints weight = 143350.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.036982 restraints weight = 73702.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.037790 restraints weight = 47779.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.038306 restraints weight = 35650.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.038658 restraints weight = 29177.312| |-----------------------------------------------------------------------------| r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21898 Z= 0.118 Angle : 0.653 14.889 30008 Z= 0.328 Chirality : 0.040 0.251 3465 Planarity : 0.004 0.058 3626 Dihedral : 7.466 129.319 3479 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.78 % Favored : 93.14 % Rotamer: Outliers : 1.91 % Allowed : 18.75 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.37 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.17), residues: 2551 helix: 0.63 (0.17), residues: 967 sheet: -0.76 (0.32), residues: 256 loop : -1.80 (0.17), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 80 TYR 0.011 0.001 TYR A 237 PHE 0.017 0.001 PHE B 15 TRP 0.020 0.001 TRP B 182 HIS 0.007 0.001 HIS A 892 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (21866) covalent geometry : angle 0.64513 / 0.33 (29980) hydrogen bonds : bond 0.04231 / 2.74 ( 832) hydrogen bonds : angle 4.44460 / 3.13 ( 2269) metal coordination : bond 0.01124 / 0.76 ( 32) metal coordination : angle 3.46349 / 2.58 ( 28) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 123 time to evaluate : 0.651 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: A 370 GLU cc_start: 0.9174 (OUTLIER) cc_final: 0.8914 (pt0) REVERT: A 380 MET cc_start: 0.9307 (mmp) cc_final: 0.9024 (mmp) REVERT: A 566 MET cc_start: 0.9260 (tpp) cc_final: 0.8890 (mmm) REVERT: A 615 MET cc_start: 0.8279 (ptm) cc_final: 0.7874 (tmm) REVERT: A 633 MET cc_start: 0.9046 (tmm) cc_final: 0.8629 (tmm) REVERT: A 668 MET cc_start: 0.9307 (tmm) cc_final: 0.8654 (tmm) REVERT: A 855 MET cc_start: 0.8634 (mtm) cc_final: 0.8130 (ptp) REVERT: A 902 MET cc_start: 0.8836 (ttt) cc_final: 0.8310 (tmm) REVERT: A 924 MET cc_start: 0.9691 (mmm) cc_final: 0.9056 (mmm) REVERT: B 49 PHE cc_start: 0.9232 (t80) cc_final: 0.8989 (m-80) REVERT: B 62 MET cc_start: 0.9192 (ppp) cc_final: 0.8864 (ppp) REVERT: B 67 MET cc_start: 0.9041 (ppp) cc_final: 0.8820 (tmm) REVERT: B 82 LYS cc_start: 0.9359 (ptpt) cc_final: 0.9095 (ptpp) REVERT: B 158 GLN cc_start: 0.9017 (tp-100) cc_final: 0.8746 (tp-100) REVERT: C 3 MET cc_start: 0.8780 (mmp) cc_final: 0.8551 (mmt) REVERT: C 70 LYS cc_start: 0.9577 (mtpp) cc_final: 0.9338 (mtmm) REVERT: D 55 MET cc_start: 0.9608 (tmm) cc_final: 0.9239 (tmm) REVERT: D 65 GLN cc_start: 0.9380 (pt0) cc_final: 0.9025 (pp30) REVERT: D 67 MET cc_start: 0.9091 (mtm) cc_final: 0.8603 (mtm) REVERT: D 70 MET cc_start: 0.9452 (tpp) cc_final: 0.8983 (tmm) REVERT: D 88 GLN cc_start: 0.9456 (mt0) cc_final: 0.9173 (mp10) REVERT: D 90 MET cc_start: 0.9571 (ttp) cc_final: 0.9287 (tmm) REVERT: D 182 TRP cc_start: 0.8270 (OUTLIER) cc_final: 0.7661 (m100) REVERT: F 68 MET cc_start: 0.8791 (pmm) cc_final: 0.8452 (pmm) REVERT: F 178 ARG cc_start: 0.7650 (mmm160) cc_final: 0.5775 (mtp85) REVERT: F 295 LEU cc_start: 0.9802 (tp) cc_final: 0.9516 (mt) REVERT: F 304 ILE cc_start: 0.9176 (mt) cc_final: 0.8848 (mm) REVERT: F 378 MET cc_start: 0.8902 (tpp) cc_final: 0.8195 (tpp) REVERT: F 429 MET cc_start: 0.9452 (tmm) cc_final: 0.8707 (ppp) REVERT: E 68 MET cc_start: 0.2448 (OUTLIER) cc_final: 0.2234 (tpt) REVERT: E 363 LEU cc_start: 0.9483 (mt) cc_final: 0.9085 (mt) REVERT: E 436 MET cc_start: 0.7969 (ptp) cc_final: 0.7652 (ptp) REVERT: E 474 MET cc_start: 0.7202 (tpt) cc_final: 0.6595 (tpt) outliers start: 42 outliers final: 32 residues processed: 157 average time/residue: 0.1439 time to fit residues: 35.5077 Evaluate side-chains 155 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 120 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain C residue 9 THR Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 268 ASN Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain F residue 332 ARG Chi-restraints excluded: chain F residue 398 TYR Chi-restraints excluded: chain F residue 436 MET Chi-restraints excluded: chain F residue 444 CYS Chi-restraints excluded: chain F residue 500 LEU Chi-restraints excluded: chain F residue 510 VAL Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 68 MET Chi-restraints excluded: chain E residue 318 CYS Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 435 ASP Chi-restraints excluded: chain E residue 464 HIS Chi-restraints excluded: chain E residue 479 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 107 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 183 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 249 optimal weight: 0.9980 chunk 192 optimal weight: 3.9990 chunk 142 optimal weight: 6.9990 chunk 204 optimal weight: 8.9990 chunk 193 optimal weight: 8.9990 chunk 141 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** 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 = 0.3428 r_free = 0.3428 target = 0.052930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.034956 restraints weight = 143952.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.036156 restraints weight = 74235.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.036956 restraints weight = 48099.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.037443 restraints weight = 36023.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.037764 restraints weight = 29698.806| |-----------------------------------------------------------------------------| r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 21898 Z= 0.171 Angle : 0.679 14.845 30008 Z= 0.342 Chirality : 0.041 0.231 3465 Planarity : 0.004 0.055 3626 Dihedral : 7.502 131.799 3479 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.19 % Favored : 91.73 % Rotamer: Outliers : 2.00 % Allowed : 18.70 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.37 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.17), residues: 2551 helix: 0.57 (0.17), residues: 977 sheet: -0.90 (0.31), residues: 275 loop : -1.86 (0.17), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 80 TYR 0.017 0.001 TYR A 237 PHE 0.027 0.001 PHE B 147 TRP 0.019 0.001 TRP B 154 HIS 0.006 0.001 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.17 (21866) covalent geometry : angle 0.66899 / 0.34 (29980) hydrogen bonds : bond 0.04256 / 2.76 ( 832) hydrogen bonds : angle 4.55831 / 3.21 ( 2269) metal coordination : bond 0.01389 / 0.91 ( 32) metal coordination : angle 3.81653 / 2.81 ( 28) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4095.18 seconds wall clock time: 71 minutes 42.59 seconds (4302.59 seconds total)