Starting phenix.real_space_refine on Sun Sep 13 07:22:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7cxn_30493/09_2026/7cxn_30493.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cxn_30493/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/7cxn_30493/09_2026/7cxn_30493.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cxn_30493/09_2026/7cxn_30493.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7cxn_30493/09_2026/7cxn_30493.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cxn_30493/09_2026/7cxn_30493.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7cxn_30493/09_2026/7cxn_30493.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7cxn_30493/09_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 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: 4.37, per 1000 atoms: 0.21 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: 2.08 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 2.98 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: 4.33 Time building geometry restraints manager: 2.68 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: 29747 4.90 - 9.79: 187 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: 12437 27.42 - 54.84: 484 54.84 - 82.26: 58 82.26 - 109.68: 4 109.68 - 137.10: 1 Dihedral angle restraints: 12984 sinusoidal: 5398 harmonic: 7586 Sorted by residual: dihedral pdb=" C4' G I 35 " pdb=" C3' G I 35 " pdb=" C2' G I 35 " pdb=" C1' G I 35 " ideal model delta sinusoidal sigma weight residual 36.34 -36.17 72.52 1 3.10e+00 1.04e-01 6.99e+02 dihedral pdb=" C4' U L 5 " pdb=" C3' U L 5 " pdb=" C2' U L 5 " pdb=" C1' U L 5 " ideal model delta sinusoidal sigma weight residual 36.34 -35.56 71.91 1 3.10e+00 1.04e-01 6.89e+02 dihedral pdb=" C4' A L 2 " pdb=" C3' A L 2 " pdb=" C2' A L 2 " pdb=" C1' A L 2 " ideal model delta sinusoidal sigma weight residual 36.34 -35.51 71.86 1 3.10e+00 1.04e-01 6.88e+02 ... (remaining 12981 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.201: 3363 0.201 - 0.403: 89 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: 5.890 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: 0.450 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 25.770 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.060 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.750 ------------------------------------------------------------------------------- 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 : 1.168 24.482 30008 Z= 0.697 Chirality : 0.074 1.006 3465 Planarity : 0.005 0.107 3626 Dihedral : 14.614 137.102 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 0.00752 / 0.39 (21866) covalent geometry : angle 1.14683 / 0.70 (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 : 0.811 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: 0.1790 time to fit residues: 47.9634 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 : 0.815 ------------------------------------------------------------------------------- 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 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 518 GLN E 519 ASN E 531 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.052208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.034070 restraints weight = 147161.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.035251 restraints weight = 75995.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.036046 restraints weight = 49711.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.036549 restraints weight = 37347.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.036864 restraints weight = 31108.470| |-----------------------------------------------------------------------------| r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 21898 Z= 0.244 Angle : 0.843 15.323 30008 Z= 0.415 Chirality : 0.049 0.408 3465 Planarity : 0.005 0.066 3626 Dihedral : 10.326 145.737 3484 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.39 % Favored : 89.38 % Rotamer: Outliers : 1.54 % Allowed : 13.07 % Favored : 85.38 % 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: -3.09 (0.15), residues: 2551 helix: -0.94 (0.16), residues: 963 sheet: -2.00 (0.28), residues: 285 loop : -3.02 (0.15), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 96 TYR 0.021 0.002 TYR A 237 PHE 0.022 0.002 PHE B 15 TRP 0.021 0.002 TRP D 182 HIS 0.015 0.001 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.24 (21866) covalent geometry : angle 0.81933 / 0.41 (29980) hydrogen bonds : bond 0.05880 / 3.77 ( 832) hydrogen bonds : angle 5.81561 / 4.11 ( 2269) metal coordination : bond 0.01862 / 1.27 ( 32) metal coordination : angle 6.57566 / 4.89 ( 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: 34 poor density : 133 time to evaluate : 0.869 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 380 MET cc_start: 0.8673 (tpp) cc_final: 0.8464 (mmt) REVERT: A 615 MET cc_start: 0.8488 (ptm) cc_final: 0.8177 (ppp) REVERT: A 633 MET cc_start: 0.9038 (tmm) cc_final: 0.8708 (tmm) REVERT: A 668 MET cc_start: 0.9491 (tmm) cc_final: 0.8847 (tmm) REVERT: B 49 PHE cc_start: 0.9360 (t80) cc_final: 0.9098 (m-80) REVERT: B 62 MET cc_start: 0.9357 (ppp) cc_final: 0.9020 (ppp) REVERT: B 67 MET cc_start: 0.9417 (ttm) cc_final: 0.9057 (tmm) REVERT: B 142 CYS cc_start: 0.8732 (p) cc_final: 0.8080 (p) REVERT: C 18 GLN cc_start: 0.9737 (tm-30) cc_final: 0.9530 (tm-30) REVERT: C 21 ARG cc_start: 0.8888 (tpp80) cc_final: 0.8681 (tpp80) REVERT: D 55 MET cc_start: 0.9596 (tmm) cc_final: 0.9234 (tmm) REVERT: D 65 GLN cc_start: 0.9415 (pt0) cc_final: 0.8926 (pp30) REVERT: D 67 MET cc_start: 0.9049 (mtm) cc_final: 0.8742 (mtm) REVERT: D 88 GLN cc_start: 0.9355 (mt0) cc_final: 0.9018 (mp10) REVERT: D 90 MET cc_start: 0.9590 (ttp) cc_final: 0.9204 (ttp) REVERT: D 94 MET cc_start: 0.8995 (mtp) cc_final: 0.8767 (mtp) REVERT: F 68 MET cc_start: 0.8943 (pmm) cc_final: 0.8559 (pmm) REVERT: F 159 SER cc_start: 0.8153 (OUTLIER) cc_final: 0.7931 (p) REVERT: F 304 ILE cc_start: 0.9137 (mt) cc_final: 0.8803 (mm) REVERT: F 378 MET cc_start: 0.8864 (tpp) cc_final: 0.8228 (tpp) REVERT: F 576 MET cc_start: 0.6816 (OUTLIER) cc_final: 0.6531 (tmm) REVERT: E 363 LEU cc_start: 0.9485 (mt) cc_final: 0.9150 (mt) outliers start: 34 outliers final: 11 residues processed: 160 average time/residue: 0.1539 time to fit residues: 38.7580 Evaluate side-chains 123 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 749 LEU 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 F residue 576 MET Chi-restraints excluded: chain E residue 165 LEU 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: 0.4980 chunk 182 optimal weight: 9.9990 chunk 144 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 94 optimal weight: 1.9990 chunk 155 optimal weight: 10.0000 chunk 135 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 213 optimal weight: 5.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 557 ASN F 559 ASN E 311 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.053176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.034995 restraints weight = 145115.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.036202 restraints weight = 74244.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.036990 restraints weight = 48082.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.037506 restraints weight = 36072.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.037781 restraints weight = 29835.831| |-----------------------------------------------------------------------------| r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 21898 Z= 0.151 Angle : 0.717 14.567 30008 Z= 0.356 Chirality : 0.046 0.300 3465 Planarity : 0.004 0.061 3626 Dihedral : 9.792 138.836 3481 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.33 % Favored : 90.51 % Rotamer: Outliers : 2.13 % Allowed : 13.62 % Favored : 84.25 % 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: -2.13 (0.16), residues: 2551 helix: -0.01 (0.17), residues: 959 sheet: -1.62 (0.30), residues: 255 loop : -2.52 (0.15), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 80 TYR 0.016 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 0.00318 / 0.15 (21866) covalent geometry : angle 0.70054 / 0.35 (29980) hydrogen bonds : bond 0.04935 / 3.15 ( 832) hydrogen bonds : angle 5.06844 / 3.56 ( 2269) metal coordination : bond 0.01391 / 0.94 ( 32) metal coordination : angle 5.04476 / 3.78 ( 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 183 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 136 time to evaluate : 0.724 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 341 VAL cc_start: 0.9694 (OUTLIER) cc_final: 0.9450 (p) REVERT: A 370 GLU cc_start: 0.9177 (OUTLIER) cc_final: 0.8906 (pt0) REVERT: A 380 MET cc_start: 0.8791 (tpp) cc_final: 0.8394 (mmt) REVERT: A 615 MET cc_start: 0.8311 (ptm) cc_final: 0.8049 (tmm) REVERT: A 633 MET cc_start: 0.9055 (tmm) cc_final: 0.8668 (tmm) REVERT: A 668 MET cc_start: 0.9430 (tmm) cc_final: 0.8822 (tmm) REVERT: A 902 MET cc_start: 0.8861 (ttt) cc_final: 0.8341 (tmm) REVERT: A 924 MET cc_start: 0.9659 (mmm) cc_final: 0.9247 (mmm) REVERT: B 67 MET cc_start: 0.9429 (ttm) cc_final: 0.9219 (tmm) REVERT: B 94 MET cc_start: 0.9339 (ttp) cc_final: 0.8795 (tmm) REVERT: C 50 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8461 (mp0) REVERT: D 48 GLU cc_start: 0.9136 (pt0) cc_final: 0.8497 (tm-30) REVERT: D 55 MET cc_start: 0.9595 (tmm) cc_final: 0.9229 (tmm) REVERT: D 65 GLN cc_start: 0.9448 (pt0) cc_final: 0.8987 (pp30) REVERT: D 67 MET cc_start: 0.9023 (mtm) cc_final: 0.8780 (mtm) REVERT: D 70 MET cc_start: 0.9403 (tpp) cc_final: 0.8977 (tmm) REVERT: D 88 GLN cc_start: 0.9349 (mt0) cc_final: 0.8990 (mp10) REVERT: D 90 MET cc_start: 0.9514 (ttp) cc_final: 0.9277 (ttp) REVERT: F 68 MET cc_start: 0.8928 (pmm) cc_final: 0.8526 (pmm) REVERT: F 304 ILE cc_start: 0.9159 (mt) cc_final: 0.8875 (mm) REVERT: F 378 MET cc_start: 0.8864 (tpp) cc_final: 0.8154 (tpp) REVERT: F 576 MET cc_start: 0.6693 (OUTLIER) cc_final: 0.6366 (tmm) REVERT: E 363 LEU cc_start: 0.9450 (mt) cc_final: 0.9090 (mt) outliers start: 47 outliers final: 19 residues processed: 175 average time/residue: 0.1439 time to fit residues: 39.2667 Evaluate side-chains 138 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 0.714 ------------------------------------------------------------------------------- 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 749 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 894 GLU 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 268 ASN 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 F residue 576 MET Chi-restraints excluded: chain E residue 183 THR 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: 0.9980 chunk 206 optimal weight: 6.9990 chunk 162 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 3 optimal weight: 0.5980 chunk 144 optimal weight: 6.9990 chunk 205 optimal weight: 7.9990 chunk 239 optimal weight: 0.0170 chunk 31 optimal weight: 2.9990 chunk 234 optimal weight: 10.0000 chunk 182 optimal weight: 7.9990 overall best weight: 2.1222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 GLN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 519 ASN E 311 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.053091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.034863 restraints weight = 145225.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.036081 restraints weight = 74453.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.036861 restraints weight = 48408.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.037368 restraints weight = 36506.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.037680 restraints weight = 30183.562| |-----------------------------------------------------------------------------| r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 21898 Z= 0.166 Angle : 0.711 14.483 30008 Z= 0.350 Chirality : 0.045 0.340 3465 Planarity : 0.004 0.057 3626 Dihedral : 9.534 136.847 3481 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.55 % Favored : 91.30 % Rotamer: Outliers : 1.95 % Allowed : 15.30 % Favored : 82.75 % 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: -1.80 (0.16), residues: 2551 helix: 0.26 (0.17), residues: 959 sheet: -1.47 (0.29), residues: 269 loop : -2.32 (0.16), residues: 1323 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 0.031 0.001 PHE E 343 TRP 0.017 0.001 TRP A 916 HIS 0.011 0.001 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.17 (21866) covalent geometry : angle 0.69474 / 0.35 (29980) hydrogen bonds : bond 0.04673 / 2.99 ( 832) hydrogen bonds : angle 4.86774 / 3.43 ( 2269) metal coordination : bond 0.01430 / 0.97 ( 32) metal coordination : angle 4.98812 / 3.74 ( 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 171 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 128 time to evaluate : 0.545 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 167 GLU cc_start: 0.9252 (tp30) cc_final: 0.9027 (tp30) REVERT: A 370 GLU cc_start: 0.9163 (OUTLIER) cc_final: 0.8926 (pt0) REVERT: A 615 MET cc_start: 0.8305 (ptm) cc_final: 0.8055 (tmm) REVERT: A 633 MET cc_start: 0.9055 (tmm) cc_final: 0.8659 (tmm) REVERT: A 668 MET cc_start: 0.9389 (tmm) cc_final: 0.8774 (tmm) REVERT: A 902 MET cc_start: 0.8821 (ttt) cc_final: 0.8366 (tmm) REVERT: B 49 PHE cc_start: 0.9272 (t80) cc_final: 0.8984 (m-80) REVERT: B 62 MET cc_start: 0.9354 (ppp) cc_final: 0.8998 (ppp) REVERT: B 67 MET cc_start: 0.9404 (ttm) cc_final: 0.9006 (tmm) REVERT: B 94 MET cc_start: 0.9296 (ttp) cc_final: 0.8961 (tmm) REVERT: D 48 GLU cc_start: 0.9184 (pt0) cc_final: 0.8597 (tm-30) REVERT: D 55 MET cc_start: 0.9597 (tmm) cc_final: 0.9230 (tmm) REVERT: D 65 GLN cc_start: 0.9453 (pt0) cc_final: 0.9079 (pp30) REVERT: D 67 MET cc_start: 0.8994 (mtm) cc_final: 0.8698 (mtm) REVERT: D 70 MET cc_start: 0.9419 (tpp) cc_final: 0.8957 (tmm) REVERT: D 88 GLN cc_start: 0.9349 (mt0) cc_final: 0.9001 (mp10) REVERT: F 68 MET cc_start: 0.8831 (pmm) cc_final: 0.8485 (pmm) REVERT: F 295 LEU cc_start: 0.9797 (OUTLIER) cc_final: 0.9541 (mt) REVERT: F 378 MET cc_start: 0.8859 (tpp) cc_final: 0.8128 (tpp) REVERT: F 576 MET cc_start: 0.6628 (OUTLIER) cc_final: 0.6304 (tmm) REVERT: E 363 LEU cc_start: 0.9493 (mt) cc_final: 0.9113 (mt) REVERT: E 436 MET cc_start: 0.7919 (ptp) cc_final: 0.7477 (ptm) outliers start: 43 outliers final: 25 residues processed: 162 average time/residue: 0.1542 time to fit residues: 38.6493 Evaluate side-chains 140 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 0.510 ------------------------------------------------------------------------------- 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 749 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 894 GLU 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 142 CYS Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain F residue 65 LEU 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 455 LEU 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 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: 4.9990 chunk 200 optimal weight: 0.7980 chunk 116 optimal weight: 9.9990 chunk 93 optimal weight: 6.9990 chunk 255 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 152 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 132 optimal weight: 0.0980 chunk 245 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 = 0.3428 r_free = 0.3428 target = 0.053245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.035037 restraints weight = 145276.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.036253 restraints weight = 74526.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.037052 restraints weight = 48528.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.037554 restraints weight = 36503.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.037886 restraints weight = 30148.786| |-----------------------------------------------------------------------------| r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2845 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= 0.154 Angle : 0.695 14.809 30008 Z= 0.342 Chirality : 0.045 0.351 3465 Planarity : 0.004 0.058 3626 Dihedral : 9.379 135.917 3481 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.31 % Favored : 91.53 % Rotamer: Outliers : 2.22 % Allowed : 16.21 % Favored : 81.57 % 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: -1.57 (0.16), residues: 2551 helix: 0.41 (0.17), residues: 959 sheet: -1.34 (0.29), residues: 274 loop : -2.16 (0.16), residues: 1318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 80 TYR 0.016 0.001 TYR A 237 PHE 0.027 0.001 PHE B 15 TRP 0.017 0.001 TRP A 916 HIS 0.009 0.001 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (21866) covalent geometry : angle 0.68090 / 0.34 (29980) hydrogen bonds : bond 0.04556 / 2.92 ( 832) hydrogen bonds : angle 4.74490 / 3.33 ( 2269) metal coordination : bond 0.01349 / 0.91 ( 32) metal coordination : angle 4.55428 / 3.40 ( 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 178 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 129 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 MET cc_start: 0.9149 (mmm) cc_final: 0.8921 (mmm) REVERT: A 370 GLU cc_start: 0.9174 (OUTLIER) cc_final: 0.8931 (pt0) REVERT: A 615 MET cc_start: 0.8353 (ptm) cc_final: 0.8085 (tmm) REVERT: A 633 MET cc_start: 0.9086 (tmm) cc_final: 0.8670 (tmm) REVERT: A 668 MET cc_start: 0.9366 (tmm) cc_final: 0.8735 (tmm) REVERT: A 818 MET cc_start: 0.8558 (ttp) cc_final: 0.8315 (ptm) REVERT: A 902 MET cc_start: 0.8850 (ttt) cc_final: 0.8401 (tmm) REVERT: A 924 MET cc_start: 0.9676 (mmm) cc_final: 0.9335 (mmm) REVERT: B 49 PHE cc_start: 0.9268 (t80) cc_final: 0.8966 (m-80) REVERT: B 62 MET cc_start: 0.9322 (ppp) cc_final: 0.9119 (ppp) REVERT: B 94 MET cc_start: 0.9375 (ttp) cc_final: 0.8973 (tmm) REVERT: D 48 GLU cc_start: 0.9188 (pt0) cc_final: 0.8543 (tm-30) REVERT: D 55 MET cc_start: 0.9607 (tmm) cc_final: 0.9240 (tmm) REVERT: D 65 GLN cc_start: 0.9451 (pt0) cc_final: 0.9054 (pp30) REVERT: D 67 MET cc_start: 0.9058 (mtm) cc_final: 0.8764 (mtm) REVERT: D 70 MET cc_start: 0.9419 (tpp) cc_final: 0.8970 (tmm) REVERT: D 88 GLN cc_start: 0.9447 (mt0) cc_final: 0.9047 (mp10) REVERT: F 68 MET cc_start: 0.8875 (pmm) cc_final: 0.8540 (pmm) REVERT: F 295 LEU cc_start: 0.9801 (OUTLIER) cc_final: 0.9541 (mt) REVERT: F 304 ILE cc_start: 0.9180 (mt) cc_final: 0.8807 (mm) REVERT: F 378 MET cc_start: 0.8861 (tpp) cc_final: 0.8134 (tpp) REVERT: F 474 MET cc_start: 0.7673 (mmt) cc_final: 0.7461 (mmp) REVERT: F 576 MET cc_start: 0.6701 (OUTLIER) cc_final: 0.6412 (tmm) REVERT: E 363 LEU cc_start: 0.9487 (mt) cc_final: 0.9101 (mt) REVERT: E 436 MET cc_start: 0.7955 (ptp) cc_final: 0.7509 (ptm) outliers start: 49 outliers final: 26 residues processed: 169 average time/residue: 0.1518 time to fit residues: 39.7190 Evaluate side-chains 147 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 118 time to evaluate : 0.518 ------------------------------------------------------------------------------- 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 463 MET Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 894 GLU 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 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 147 LEU 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 455 LEU 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 340 VAL Chi-restraints excluded: chain E residue 376 ILE 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: 0.8980 chunk 18 optimal weight: 1.9990 chunk 254 optimal weight: 0.9990 chunk 130 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 202 optimal weight: 9.9990 chunk 124 optimal weight: 5.9990 chunk 217 optimal weight: 6.9990 chunk 147 optimal weight: 0.2980 chunk 250 optimal weight: 10.0000 overall best weight: 1.8386 ------------------------------------------------------------------------------- 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 562 ASN ** 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 = 0.3434 r_free = 0.3434 target = 0.053408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.035249 restraints weight = 145146.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.036454 restraints weight = 74084.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.037257 restraints weight = 47760.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.037772 restraints weight = 36026.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 62)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.038113 restraints weight = 29789.685| |-----------------------------------------------------------------------------| r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21898 Z= 0.149 Angle : 0.691 14.686 30008 Z= 0.340 Chirality : 0.044 0.353 3465 Planarity : 0.004 0.058 3626 Dihedral : 9.270 135.426 3481 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.92 % Favored : 91.96 % Rotamer: Outliers : 2.86 % Allowed : 15.98 % Favored : 81.16 % 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: -1.42 (0.16), residues: 2551 helix: 0.47 (0.17), residues: 962 sheet: -1.12 (0.29), residues: 280 loop : -2.07 (0.17), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 96 TYR 0.015 0.001 TYR A 237 PHE 0.026 0.001 PHE B 15 TRP 0.017 0.001 TRP A 916 HIS 0.008 0.001 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 (21866) covalent geometry : angle 0.67882 / 0.34 (29980) hydrogen bonds : bond 0.04457 / 2.86 ( 832) hydrogen bonds : angle 4.65070 / 3.26 ( 2269) metal coordination : bond 0.01283 / 0.87 ( 32) metal coordination : angle 4.25700 / 3.18 ( 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 190 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 127 time to evaluate : 0.824 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: 0.9178 (OUTLIER) cc_final: 0.8937 (pt0) REVERT: A 377 ASP cc_start: 0.8706 (t0) cc_final: 0.8395 (t0) REVERT: A 633 MET cc_start: 0.9084 (tmm) cc_final: 0.8676 (tmm) REVERT: A 668 MET cc_start: 0.9344 (tmm) cc_final: 0.8713 (tmm) REVERT: A 902 MET cc_start: 0.8842 (ttt) cc_final: 0.8248 (tmm) REVERT: A 924 MET cc_start: 0.9659 (mmm) cc_final: 0.9171 (mmm) REVERT: B 49 PHE cc_start: 0.9258 (t80) cc_final: 0.8977 (m-80) REVERT: B 97 LYS cc_start: 0.9512 (pttp) cc_final: 0.9286 (pptt) REVERT: D 48 GLU cc_start: 0.9182 (pt0) cc_final: 0.8557 (tm-30) REVERT: D 55 MET cc_start: 0.9606 (tmm) cc_final: 0.9232 (tmm) REVERT: D 65 GLN cc_start: 0.9449 (pt0) cc_final: 0.9069 (pp30) REVERT: D 67 MET cc_start: 0.9055 (mtm) cc_final: 0.8702 (mtm) REVERT: D 70 MET cc_start: 0.9421 (tpp) cc_final: 0.8994 (tmm) REVERT: D 88 GLN cc_start: 0.9403 (mt0) cc_final: 0.9178 (mp10) REVERT: F 68 MET cc_start: 0.8837 (pmm) cc_final: 0.8512 (pmm) REVERT: F 295 LEU cc_start: 0.9802 (OUTLIER) cc_final: 0.9515 (mt) REVERT: F 304 ILE cc_start: 0.9166 (mt) cc_final: 0.8798 (mm) REVERT: F 378 MET cc_start: 0.8883 (tpp) cc_final: 0.8158 (tpp) REVERT: F 576 MET cc_start: 0.6892 (OUTLIER) cc_final: 0.6593 (tmm) REVERT: E 274 MET cc_start: 0.9140 (tpt) cc_final: 0.8715 (tpp) REVERT: E 363 LEU cc_start: 0.9488 (mt) cc_final: 0.9094 (mt) REVERT: E 436 MET cc_start: 0.8001 (ptp) cc_final: 0.7553 (ptm) outliers start: 63 outliers final: 41 residues processed: 180 average time/residue: 0.1527 time to fit residues: 43.4182 Evaluate side-chains 163 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 119 time to evaluate : 0.799 ------------------------------------------------------------------------------- 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 463 MET Chi-restraints excluded: chain A residue 464 CYS 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 854 LEU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 894 GLU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 15 PHE 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 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 455 LEU 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 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 474 MET 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: 1.9990 chunk 22 optimal weight: 10.0000 chunk 158 optimal weight: 10.0000 chunk 211 optimal weight: 1.9990 chunk 194 optimal weight: 8.9990 chunk 24 optimal weight: 0.2980 chunk 120 optimal weight: 4.9990 chunk 227 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 ASN ** A 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 311 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.053102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.034991 restraints weight = 144989.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.036194 restraints weight = 74552.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.036979 restraints weight = 48307.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.037468 restraints weight = 36342.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.037811 restraints weight = 30123.929| |-----------------------------------------------------------------------------| r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21898 Z= 0.167 Angle : 0.706 14.626 30008 Z= 0.346 Chirality : 0.045 0.346 3465 Planarity : 0.004 0.057 3626 Dihedral : 9.266 135.942 3481 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.47 % Favored : 91.42 % Rotamer: Outliers : 2.54 % Allowed : 16.89 % Favored : 80.57 % 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: -1.38 (0.16), residues: 2551 helix: 0.49 (0.17), residues: 968 sheet: -1.02 (0.30), residues: 262 loop : -2.05 (0.16), residues: 1321 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 0.024 0.001 PHE B 15 TRP 0.016 0.001 TRP A 916 HIS 0.008 0.001 HIS A 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.17 (21866) covalent geometry : angle 0.69419 / 0.34 (29980) hydrogen bonds : bond 0.04434 / 2.86 ( 832) hydrogen bonds : angle 4.63055 / 3.25 ( 2269) metal coordination : bond 0.01388 / 0.92 ( 32) metal coordination : angle 4.18548 / 3.10 ( 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 177 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 121 time to evaluate : 0.893 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: 0.9181 (OUTLIER) cc_final: 0.8937 (pt0) REVERT: A 377 ASP cc_start: 0.8714 (t0) cc_final: 0.8379 (t0) REVERT: A 633 MET cc_start: 0.9127 (tmm) cc_final: 0.8689 (tmm) REVERT: A 668 MET cc_start: 0.9348 (tmm) cc_final: 0.8709 (tmm) REVERT: A 902 MET cc_start: 0.8867 (ttt) cc_final: 0.8286 (tmm) REVERT: A 924 MET cc_start: 0.9678 (mmm) cc_final: 0.9149 (mmm) REVERT: B 49 PHE cc_start: 0.9236 (t80) cc_final: 0.8958 (m-80) REVERT: B 94 MET cc_start: 0.9372 (ttp) cc_final: 0.8884 (tmm) REVERT: B 97 LYS cc_start: 0.9522 (pttp) cc_final: 0.9306 (pptt) REVERT: D 48 GLU cc_start: 0.9179 (pt0) cc_final: 0.8538 (tm-30) REVERT: D 55 MET cc_start: 0.9611 (tmm) cc_final: 0.9233 (tmm) REVERT: D 65 GLN cc_start: 0.9442 (pt0) cc_final: 0.9074 (pp30) REVERT: D 67 MET cc_start: 0.9093 (mtm) cc_final: 0.8741 (mtm) REVERT: D 70 MET cc_start: 0.9434 (tpp) cc_final: 0.8992 (tmm) REVERT: D 88 GLN cc_start: 0.9511 (mt0) cc_final: 0.9159 (mp10) REVERT: D 90 MET cc_start: 0.9593 (ttp) cc_final: 0.9210 (tmm) REVERT: F 68 MET cc_start: 0.8853 (pmm) cc_final: 0.8513 (pmm) REVERT: F 295 LEU cc_start: 0.9803 (OUTLIER) cc_final: 0.9531 (mt) REVERT: F 304 ILE cc_start: 0.9175 (mt) cc_final: 0.8832 (mm) REVERT: F 378 MET cc_start: 0.8875 (tpp) cc_final: 0.8150 (tpp) REVERT: F 576 MET cc_start: 0.6860 (OUTLIER) cc_final: 0.6583 (tmm) REVERT: E 274 MET cc_start: 0.9061 (tpt) cc_final: 0.8676 (tpp) REVERT: E 363 LEU cc_start: 0.9499 (mt) cc_final: 0.9096 (mt) REVERT: E 436 MET cc_start: 0.8068 (ptp) cc_final: 0.7605 (ptm) outliers start: 56 outliers final: 40 residues processed: 167 average time/residue: 0.1569 time to fit residues: 41.2431 Evaluate side-chains 160 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 117 time to evaluate : 0.843 ------------------------------------------------------------------------------- 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 464 CYS 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 854 LEU Chi-restraints excluded: chain A residue 894 GLU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 15 PHE Chi-restraints excluded: chain B residue 61 LYS 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 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 247 VAL 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 455 LEU 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 183 THR 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 474 MET 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: 9.9990 chunk 94 optimal weight: 40.0000 chunk 120 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 101 optimal weight: 7.9990 chunk 36 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 171 optimal weight: 7.9990 chunk 84 optimal weight: 0.7980 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 ASN A 543 ASN ** A 570 GLN ** 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 ** F 562 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 = 0.3439 r_free = 0.3439 target = 0.053539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.035443 restraints weight = 143567.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.036654 restraints weight = 73562.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.037467 restraints weight = 47830.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 65)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.037974 restraints weight = 35801.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.038292 restraints weight = 29559.364| |-----------------------------------------------------------------------------| r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21898 Z= 0.136 Angle : 0.682 14.656 30008 Z= 0.333 Chirality : 0.044 0.329 3465 Planarity : 0.004 0.057 3626 Dihedral : 9.185 136.237 3481 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.60 % Favored : 92.32 % Rotamer: Outliers : 2.09 % Allowed : 17.16 % Favored : 80.75 % 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: -1.27 (0.16), residues: 2551 helix: 0.52 (0.17), residues: 976 sheet: -0.97 (0.30), residues: 269 loop : -1.94 (0.17), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 80 TYR 0.013 0.001 TYR A 237 PHE 0.024 0.001 PHE B 15 TRP 0.017 0.001 TRP B 182 HIS 0.006 0.001 HIS A 892 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (21866) covalent geometry : angle 0.67208 / 0.33 (29980) hydrogen bonds : bond 0.04378 / 2.84 ( 832) hydrogen bonds : angle 4.50694 / 3.16 ( 2269) metal coordination : bond 0.01186 / 0.80 ( 32) metal coordination : angle 3.79976 / 2.81 ( 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 179 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 133 time to evaluate : 0.752 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: 0.9178 (OUTLIER) cc_final: 0.8932 (pt0) REVERT: A 377 ASP cc_start: 0.8578 (t0) cc_final: 0.8236 (t0) REVERT: A 615 MET cc_start: 0.8553 (tmm) cc_final: 0.8319 (tmm) REVERT: A 633 MET cc_start: 0.9088 (tmm) cc_final: 0.8671 (tmm) REVERT: A 668 MET cc_start: 0.9337 (tmm) cc_final: 0.8715 (tmm) REVERT: A 703 ASN cc_start: 0.8884 (m110) cc_final: 0.8615 (m110) REVERT: A 902 MET cc_start: 0.8847 (ttt) cc_final: 0.8304 (tmm) REVERT: A 924 MET cc_start: 0.9684 (mmm) cc_final: 0.9109 (mmm) REVERT: B 49 PHE cc_start: 0.9229 (t80) cc_final: 0.8938 (m-80) REVERT: B 62 MET cc_start: 0.9321 (ppp) cc_final: 0.8879 (ppp) REVERT: B 94 MET cc_start: 0.9397 (ttp) cc_final: 0.8898 (tmm) REVERT: C 70 LYS cc_start: 0.9356 (mtmm) cc_final: 0.9115 (mtmt) REVERT: D 48 GLU cc_start: 0.9197 (pt0) cc_final: 0.8611 (tm-30) REVERT: D 55 MET cc_start: 0.9607 (tmm) cc_final: 0.9225 (tmm) REVERT: D 65 GLN cc_start: 0.9412 (pt0) cc_final: 0.9073 (pp30) REVERT: D 67 MET cc_start: 0.9093 (mtm) cc_final: 0.8751 (mtm) REVERT: D 70 MET cc_start: 0.9425 (tpp) cc_final: 0.8985 (tmm) REVERT: D 88 GLN cc_start: 0.9491 (mt0) cc_final: 0.9217 (mp10) REVERT: D 90 MET cc_start: 0.9577 (ttp) cc_final: 0.9241 (tmm) REVERT: F 178 ARG cc_start: 0.8353 (tpp80) cc_final: 0.7957 (mmm-85) REVERT: F 295 LEU cc_start: 0.9805 (OUTLIER) cc_final: 0.9524 (mt) REVERT: F 304 ILE cc_start: 0.9167 (mt) cc_final: 0.8830 (mm) REVERT: F 378 MET cc_start: 0.8889 (tpp) cc_final: 0.8179 (tpp) REVERT: F 474 MET cc_start: 0.7229 (mmt) cc_final: 0.6925 (mmp) REVERT: F 576 MET cc_start: 0.6984 (OUTLIER) cc_final: 0.6704 (tmm) REVERT: E 274 MET cc_start: 0.9074 (tpt) cc_final: 0.8676 (tpp) REVERT: E 363 LEU cc_start: 0.9460 (mt) cc_final: 0.9061 (mt) REVERT: E 436 MET cc_start: 0.8038 (ptp) cc_final: 0.7615 (ptm) REVERT: E 561 PHE cc_start: 0.9415 (t80) cc_final: 0.9165 (t80) outliers start: 46 outliers final: 37 residues processed: 170 average time/residue: 0.1592 time to fit residues: 42.3801 Evaluate side-chains 160 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 120 time to evaluate : 0.811 ------------------------------------------------------------------------------- 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 464 CYS 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 854 LEU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 15 PHE 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 127 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 247 VAL 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 455 LEU 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 318 CYS Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 401 ASP Chi-restraints excluded: chain E residue 464 HIS Chi-restraints excluded: chain E residue 474 MET 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: 4.9990 chunk 135 optimal weight: 10.0000 chunk 152 optimal weight: 5.9990 chunk 247 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 144 optimal weight: 0.8980 chunk 68 optimal weight: 7.9990 chunk 121 optimal weight: 10.0000 chunk 138 optimal weight: 9.9990 chunk 186 optimal weight: 10.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 81 GLN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 886 GLN B 158 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 = 0.3403 r_free = 0.3403 target = 0.052195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.034237 restraints weight = 145422.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.035390 restraints weight = 75319.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.036152 restraints weight = 49268.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.036660 restraints weight = 37369.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.036970 restraints weight = 31001.142| |-----------------------------------------------------------------------------| r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 21898 Z= 0.235 Angle : 0.758 14.582 30008 Z= 0.370 Chirality : 0.046 0.326 3465 Planarity : 0.004 0.056 3626 Dihedral : 9.331 135.282 3481 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.49 % Favored : 90.44 % Rotamer: Outliers : 2.50 % Allowed : 17.48 % 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: -1.39 (0.16), residues: 2551 helix: 0.45 (0.17), residues: 976 sheet: -1.24 (0.30), residues: 274 loop : -1.99 (0.17), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 80 TYR 0.021 0.001 TYR A 237 PHE 0.023 0.002 PHE B 15 TRP 0.013 0.002 TRP F 167 HIS 0.008 0.001 HIS A 892 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.23 (21866) covalent geometry : angle 0.74604 / 0.37 (29980) hydrogen bonds : bond 0.04577 / 2.97 ( 832) hydrogen bonds : angle 4.76304 / 3.35 ( 2269) metal coordination : bond 0.01915 / 1.21 ( 32) metal coordination : angle 4.40832 / 3.23 ( 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 176 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 121 time to evaluate : 0.791 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: 0.9163 (OUTLIER) cc_final: 0.8921 (pt0) REVERT: A 377 ASP cc_start: 0.8623 (t0) cc_final: 0.8330 (t0) REVERT: A 633 MET cc_start: 0.9111 (tmm) cc_final: 0.8770 (tmm) REVERT: A 668 MET cc_start: 0.9359 (tmm) cc_final: 0.8687 (tmm) REVERT: A 902 MET cc_start: 0.8829 (ttt) cc_final: 0.8314 (tmm) REVERT: A 924 MET cc_start: 0.9672 (mmm) cc_final: 0.9102 (mmm) REVERT: B 49 PHE cc_start: 0.9225 (t80) cc_final: 0.8947 (m-80) REVERT: B 62 MET cc_start: 0.9371 (ppp) cc_final: 0.8983 (ppp) REVERT: B 158 GLN cc_start: 0.9072 (tp-100) cc_final: 0.8811 (tp-100) REVERT: C 3 MET cc_start: 0.8664 (mmp) cc_final: 0.8308 (mmt) REVERT: C 70 LYS cc_start: 0.9316 (mtmm) cc_final: 0.9079 (mtmt) REVERT: D 55 MET cc_start: 0.9601 (tmm) cc_final: 0.9206 (tmm) REVERT: D 65 GLN cc_start: 0.9435 (pt0) cc_final: 0.9073 (pp30) REVERT: D 67 MET cc_start: 0.9072 (mtm) cc_final: 0.8701 (mtm) REVERT: D 70 MET cc_start: 0.9435 (tpp) cc_final: 0.9006 (tmm) REVERT: D 88 GLN cc_start: 0.9490 (mt0) cc_final: 0.9153 (mp10) REVERT: D 90 MET cc_start: 0.9572 (ttp) cc_final: 0.9304 (tmm) REVERT: F 68 MET cc_start: 0.8751 (pmm) cc_final: 0.8220 (pmm) REVERT: F 295 LEU cc_start: 0.9808 (OUTLIER) cc_final: 0.9536 (mt) REVERT: F 304 ILE cc_start: 0.9228 (mt) cc_final: 0.8893 (mm) REVERT: F 378 MET cc_start: 0.8884 (tpp) cc_final: 0.8167 (tpp) REVERT: F 474 MET cc_start: 0.7317 (mmt) cc_final: 0.7023 (mmp) REVERT: F 576 MET cc_start: 0.6989 (OUTLIER) cc_final: 0.6574 (tmm) REVERT: E 363 LEU cc_start: 0.9534 (mt) cc_final: 0.9123 (mt) REVERT: E 436 MET cc_start: 0.8051 (ptp) cc_final: 0.7553 (ptm) outliers start: 55 outliers final: 40 residues processed: 166 average time/residue: 0.1468 time to fit residues: 38.3752 Evaluate side-chains 161 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 118 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 315 VAL 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 749 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 854 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 15 PHE 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 142 CYS Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 247 VAL 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 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 561 PHE Chi-restraints excluded: chain F residue 576 MET 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 474 MET 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: 2.9990 chunk 10 optimal weight: 3.9990 chunk 181 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 162 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 211 optimal weight: 5.9990 chunk 246 optimal weight: 7.9990 chunk 206 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 173 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 79 ASN ** 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 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 311 HIS E 531 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.053344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.034815 restraints weight = 138271.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.036023 restraints weight = 70071.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.036830 restraints weight = 45563.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.037371 restraints weight = 34263.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.037679 restraints weight = 28259.771| |-----------------------------------------------------------------------------| r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.3614 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= 0.129 Angle : 0.702 14.680 30008 Z= 0.343 Chirality : 0.045 0.303 3465 Planarity : 0.004 0.058 3626 Dihedral : 9.156 136.068 3479 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.13 % Favored : 92.79 % Rotamer: Outliers : 1.86 % Allowed : 18.29 % Favored : 79.85 % 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: -1.16 (0.17), residues: 2551 helix: 0.59 (0.17), residues: 974 sheet: -0.84 (0.31), residues: 256 loop : -1.86 (0.17), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 80 TYR 0.012 0.001 TYR A 237 PHE 0.025 0.001 PHE E 343 TRP 0.022 0.001 TRP B 182 HIS 0.007 0.001 HIS A 892 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (21866) covalent geometry : angle 0.69312 / 0.34 (29980) hydrogen bonds : bond 0.04469 / 2.91 ( 832) hydrogen bonds : angle 4.53245 / 3.18 ( 2269) metal coordination : bond 0.01176 / 0.80 ( 32) metal coordination : angle 3.68840 / 2.73 ( 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 168 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 127 time to evaluate : 0.729 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: 0.9178 (OUTLIER) cc_final: 0.8923 (pt0) REVERT: A 377 ASP cc_start: 0.8510 (t0) cc_final: 0.8183 (t0) REVERT: A 633 MET cc_start: 0.9000 (tmm) cc_final: 0.8599 (tmm) REVERT: A 668 MET cc_start: 0.9335 (tmm) cc_final: 0.8720 (tmm) REVERT: A 703 ASN cc_start: 0.8840 (m110) cc_final: 0.8583 (m110) REVERT: A 902 MET cc_start: 0.8808 (ttt) cc_final: 0.8303 (tmm) REVERT: A 924 MET cc_start: 0.9667 (mmm) cc_final: 0.9087 (mmm) REVERT: B 49 PHE cc_start: 0.9237 (t80) cc_final: 0.8958 (m-80) REVERT: B 62 MET cc_start: 0.9352 (ppp) cc_final: 0.8869 (ppp) REVERT: B 65 GLN cc_start: 0.9654 (pp30) cc_final: 0.8994 (pp30) REVERT: B 158 GLN cc_start: 0.9006 (tp-100) cc_final: 0.8731 (tp-100) REVERT: C 3 MET cc_start: 0.8617 (mmp) cc_final: 0.8385 (mmt) REVERT: C 70 LYS cc_start: 0.9396 (mtmm) cc_final: 0.9142 (mtmt) REVERT: D 55 MET cc_start: 0.9608 (tmm) cc_final: 0.9227 (tmm) REVERT: D 65 GLN cc_start: 0.9420 (pt0) cc_final: 0.9045 (pp30) REVERT: D 67 MET cc_start: 0.9062 (mtm) cc_final: 0.8580 (mtm) REVERT: D 70 MET cc_start: 0.9427 (tpp) cc_final: 0.8982 (tmm) REVERT: D 90 MET cc_start: 0.9550 (ttp) cc_final: 0.9271 (tmm) REVERT: F 295 LEU cc_start: 0.9808 (OUTLIER) cc_final: 0.9514 (mt) REVERT: F 304 ILE cc_start: 0.9176 (mt) cc_final: 0.8834 (mm) REVERT: F 378 MET cc_start: 0.8889 (tpp) cc_final: 0.8178 (tpp) REVERT: F 429 MET cc_start: 0.9466 (tmm) cc_final: 0.8685 (ppp) REVERT: F 474 MET cc_start: 0.7232 (mmt) cc_final: 0.6947 (mmp) REVERT: F 576 MET cc_start: 0.7005 (OUTLIER) cc_final: 0.6588 (tmm) REVERT: E 68 MET cc_start: 0.0878 (tpt) cc_final: 0.0490 (tpt) REVERT: E 363 LEU cc_start: 0.9471 (mt) cc_final: 0.9070 (mt) REVERT: E 436 MET cc_start: 0.8043 (ptp) cc_final: 0.7616 (ptm) outliers start: 41 outliers final: 32 residues processed: 158 average time/residue: 0.1528 time to fit residues: 38.2810 Evaluate side-chains 157 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 122 time to evaluate : 0.795 ------------------------------------------------------------------------------- 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 794 MET Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain B residue 15 PHE 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 142 CYS Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain F residue 247 VAL 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 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 561 PHE Chi-restraints excluded: chain F residue 576 MET Chi-restraints excluded: chain E residue 318 CYS Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 401 ASP Chi-restraints excluded: chain E residue 464 HIS Chi-restraints excluded: chain E residue 474 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 107 optimal weight: 3.9990 chunk 22 optimal weight: 0.0870 chunk 183 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 249 optimal weight: 9.9990 chunk 192 optimal weight: 5.9990 chunk 142 optimal weight: 0.3980 chunk 204 optimal weight: 7.9990 chunk 193 optimal weight: 9.9990 chunk 141 optimal weight: 0.3980 overall best weight: 1.5762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 GLN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 311 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.053454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.035415 restraints weight = 143970.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.036601 restraints weight = 74491.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.037391 restraints weight = 48485.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.037906 restraints weight = 36489.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.038231 restraints weight = 30048.428| |-----------------------------------------------------------------------------| r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.3723 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= 0.140 Angle : 0.707 14.674 30008 Z= 0.344 Chirality : 0.045 0.294 3465 Planarity : 0.004 0.064 3626 Dihedral : 9.108 135.432 3479 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.88 % Favored : 92.04 % Rotamer: Outliers : 1.82 % Allowed : 18.52 % Favored : 79.66 % 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: -1.10 (0.17), residues: 2551 helix: 0.62 (0.17), residues: 970 sheet: -0.79 (0.31), residues: 262 loop : -1.82 (0.17), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 80 TYR 0.028 0.001 TYR F 180 PHE 0.031 0.001 PHE B 147 TRP 0.040 0.002 TRP F 167 HIS 0.007 0.001 HIS A 892 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (21866) covalent geometry : angle 0.69839 / 0.34 (29980) hydrogen bonds : bond 0.04379 / 2.85 ( 832) hydrogen bonds : angle 4.50599 / 3.17 ( 2269) metal coordination : bond 0.01196 / 0.81 ( 32) metal coordination : angle 3.63032 / 2.70 ( 28) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4408.23 seconds wall clock time: 77 minutes 13.71 seconds (4633.71 seconds total)