Starting phenix.real_space_refine on Fri Sep 19 00:54:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cxn_30493/09_2025/7cxn_30493.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cxn_30493/09_2025/7cxn_30493.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7cxn_30493/09_2025/7cxn_30493.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cxn_30493/09_2025/7cxn_30493.map" model { file = "/net/cci-nas-00/data/ceres_data/7cxn_30493/09_2025/7cxn_30493.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cxn_30493/09_2025/7cxn_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-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21295 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 926, 7458 Classifications: {'peptide': 926} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 895} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 1396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1396 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 6, 'TRANS': 180} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'TYR:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "C" Number of atoms: 553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 553 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Chain: "D" Number of atoms: 1414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1414 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 179} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "I" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 545 Classifications: {'RNA': 25} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 16, 'rna3p_pyr': 8} Link IDs: {'rna3p': 24} Chain: "J" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 545 Classifications: {'RNA': 26} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 9, 'rna3p_pyr': 16} Link IDs: {'rna2p': 1, 'rna3p': 24} Chain: "L" Number of atoms: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 128 Classifications: {'RNA': 6} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 1, 'rna3p_pyr': 1} Link IDs: {'rna2p': 3, 'rna3p': 2} Chain: "F" Number of atoms: 4630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4630 Classifications: {'peptide': 596} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 5, 'PTRANS': 30, 'TRANS': 560} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 4618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4618 Classifications: {'peptide': 596} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 4, 'PTRANS': 30, 'TRANS': 561} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 27 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2446 SG CYS A 301 59.044 66.687 125.669 1.00120.79 S ATOM 2487 SG CYS A 306 58.337 66.866 129.473 1.00109.02 S ATOM 2519 SG CYS A 310 61.753 65.606 128.086 1.00106.10 S ATOM 3927 SG CYS A 487 48.124 78.989 112.682 1.00132.82 S ATOM 5180 SG CYS A 645 47.855 80.227 116.275 1.00129.11 S ATOM 5186 SG CYS A 646 48.897 76.635 115.582 1.00129.46 S ATOM 12066 SG CYS F 5 38.526 77.166 65.507 1.00197.03 S ATOM 12087 SG CYS F 8 39.371 79.862 62.949 1.00196.81 S ATOM 12225 SG CYS F 26 36.565 80.652 64.966 1.00207.13 S ATOM 12246 SG CYS F 29 35.663 78.053 63.206 1.00212.00 S ATOM 12411 SG CYS F 50 23.804 84.901 87.278 1.00252.93 S ATOM 12441 SG CYS F 55 20.831 82.494 87.526 1.00257.68 S ATOM 12574 SG CYS F 72 20.226 85.818 86.079 1.00263.37 S ATOM 12148 SG CYS F 16 31.023 72.587 73.118 1.00204.79 S ATOM 12163 SG CYS F 19 32.116 69.541 71.286 1.00214.40 S ATOM 16696 SG CYS E 5 77.272 115.943 58.881 1.00140.71 S ATOM 16717 SG CYS E 8 79.506 119.058 58.914 1.00146.09 S ATOM 16855 SG CYS E 26 75.589 119.357 59.219 1.00149.43 S ATOM 16876 SG CYS E 29 76.948 118.751 56.213 1.00156.27 S ATOM 17041 SG CYS E 50 49.379 115.931 58.356 1.00185.29 S ATOM 17071 SG CYS E 55 49.243 116.075 54.577 1.00193.67 S ATOM 17204 SG CYS E 72 48.122 119.109 56.517 1.00184.60 S ATOM 16778 SG CYS E 16 68.067 112.253 51.573 1.00144.79 S ATOM 16793 SG CYS E 19 70.696 110.872 49.344 1.00147.10 S Time building chain proxies: 5.16, per 1000 atoms: 0.24 Number of scatterers: 21295 At special positions: 0 Unit cell: (139.4, 159.9, 187.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 8 29.99 S 149 16.00 P 57 15.00 O 4175 8.00 N 3614 7.00 C 13292 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.99 Conformation dependent library (CDL) restraints added in 990.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 2.94 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: 4.46 Time building geometry restraints manager: 2.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6508 1.33 - 1.46: 5384 1.46 - 1.58: 9653 1.58 - 1.71: 111 1.71 - 1.83: 210 Bond restraints: 21866 Sorted by residual: bond pdb=" CA LEU A 302 " pdb=" CB LEU A 302 " ideal model delta sigma weight residual 1.531 1.361 0.170 1.57e-02 4.06e+03 1.17e+02 bond pdb=" CA ASP A 303 " pdb=" CB ASP A 303 " ideal model delta sigma weight residual 1.526 1.414 0.113 1.28e-02 6.10e+03 7.75e+01 bond pdb=" CA TRP A 509 " pdb=" C TRP A 509 " ideal model delta sigma weight residual 1.523 1.453 0.070 1.34e-02 5.57e+03 2.73e+01 bond pdb=" N GLY A 510 " pdb=" CA GLY A 510 " ideal model delta sigma weight residual 1.447 1.508 -0.061 1.19e-02 7.06e+03 2.60e+01 bond pdb=" CA LYS A 718 " pdb=" C LYS A 718 " ideal model delta sigma weight residual 1.523 1.461 0.062 1.34e-02 5.57e+03 2.17e+01 ... (remaining 21861 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.90: 29750 4.90 - 9.79: 184 9.79 - 14.69: 33 14.69 - 19.59: 12 19.59 - 24.48: 1 Bond angle restraints: 29980 Sorted by residual: angle pdb=" N ILE E 333 " pdb=" CA ILE E 333 " pdb=" C ILE E 333 " ideal model delta sigma weight residual 111.81 125.42 -13.61 8.60e-01 1.35e+00 2.51e+02 angle pdb=" N ASP A 303 " pdb=" CA ASP A 303 " pdb=" CB ASP A 303 " ideal model delta sigma weight residual 108.96 128.27 -19.31 1.23e+00 6.61e-01 2.46e+02 angle pdb=" N PHE A 275 " pdb=" CA PHE A 275 " pdb=" C PHE A 275 " ideal model delta sigma weight residual 111.54 129.11 -17.57 1.36e+00 5.41e-01 1.67e+02 angle pdb=" N VAL F 348 " pdb=" CA VAL F 348 " pdb=" C VAL F 348 " ideal model delta sigma weight residual 111.58 124.09 -12.51 1.06e+00 8.90e-01 1.39e+02 angle pdb=" N GLN D 157 " pdb=" CA GLN D 157 " pdb=" CB GLN D 157 " ideal model delta sigma weight residual 110.90 95.33 15.57 1.33e+00 5.65e-01 1.37e+02 ... (remaining 29975 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.42: 12585 27.42 - 54.84: 486 54.84 - 82.26: 107 82.26 - 109.68: 5 109.68 - 137.10: 1 Dihedral angle restraints: 13184 sinusoidal: 5598 harmonic: 7586 Sorted by residual: dihedral pdb=" C ASP E 344 " pdb=" N ASP E 344 " pdb=" CA ASP E 344 " pdb=" CB ASP E 344 " ideal model delta harmonic sigma weight residual -122.60 -144.90 22.30 0 2.50e+00 1.60e-01 7.95e+01 dihedral pdb=" N ASP E 344 " pdb=" C ASP E 344 " pdb=" CA ASP E 344 " pdb=" CB ASP E 344 " ideal model delta harmonic sigma weight residual 122.80 143.05 -20.25 0 2.50e+00 1.60e-01 6.56e+01 dihedral pdb=" N ASP A 303 " pdb=" C ASP A 303 " pdb=" CA ASP A 303 " pdb=" CB ASP A 303 " ideal model delta harmonic sigma weight residual 122.80 141.10 -18.30 0 2.50e+00 1.60e-01 5.36e+01 ... (remaining 13181 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.201: 3416 0.201 - 0.403: 36 0.403 - 0.604: 8 0.604 - 0.805: 3 0.805 - 1.006: 2 Chirality restraints: 3465 Sorted by residual: chirality pdb=" CA ASP E 344 " pdb=" N ASP E 344 " pdb=" C ASP E 344 " pdb=" CB ASP E 344 " both_signs ideal model delta sigma weight residual False 2.51 1.50 1.01 2.00e-01 2.50e+01 2.53e+01 chirality pdb=" CA LEU A 302 " pdb=" N LEU A 302 " pdb=" C LEU A 302 " pdb=" CB LEU A 302 " both_signs ideal model delta sigma weight residual False 2.51 1.64 0.87 2.00e-01 2.50e+01 1.88e+01 chirality pdb=" CA ASP A 303 " pdb=" N ASP A 303 " pdb=" C ASP A 303 " pdb=" CB ASP A 303 " both_signs ideal model delta sigma weight residual False 2.51 1.72 0.80 2.00e-01 2.50e+01 1.58e+01 ... (remaining 3462 not shown) Planarity restraints: 3626 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP B 182 " 0.071 5.00e-02 4.00e+02 1.07e-01 1.84e+01 pdb=" N PRO B 183 " -0.185 5.00e-02 4.00e+02 pdb=" CA PRO B 183 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO B 183 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG F 173 " 0.038 5.00e-02 4.00e+02 5.87e-02 5.51e+00 pdb=" N PRO F 174 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO F 174 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO F 174 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 132 " -0.038 5.00e-02 4.00e+02 5.81e-02 5.41e+00 pdb=" N PRO B 133 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO B 133 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 133 " -0.032 5.00e-02 4.00e+02 ... (remaining 3623 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 247 2.42 - 3.04: 15799 3.04 - 3.66: 34744 3.66 - 4.28: 49695 4.28 - 4.90: 75997 Nonbonded interactions: 176482 Sorted by model distance: nonbonded pdb=" CD ARG F 332 " pdb=" O LYS F 347 " model vdw 1.804 3.440 nonbonded pdb=" ND2 ASN F 124 " pdb=" O TYR F 421 " model vdw 1.977 3.120 nonbonded pdb=" OG1 THR E 153 " pdb=" OG SER E 166 " model vdw 2.044 3.040 nonbonded pdb=" O ASP A 846 " pdb=" OG1 THR A 850 " model vdw 2.049 3.040 nonbonded pdb=" O ASP E 260 " pdb=" OG SER E 263 " model vdw 2.087 3.040 ... (remaining 176477 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and ((resid 6 through 8 and (name N or name CA or name C or name O or \ name CB )) or resid 9 through 22 or (resid 23 through 28 and (name N or name CA \ or name C or name O or name CB )) or resid 29 through 191)) selection = (chain 'D' and (resid 6 through 21 or (resid 22 through 28 and (name N or name C \ A or name C or name O or name CB )) or resid 29 through 31 or (resid 32 and (nam \ e N or name CA or name C or name O or name CB )) or resid 33 through 34 or (resi \ d 35 through 37 and (name N or name CA or name C or name O or name CB )) or resi \ d 38 or (resid 39 through 40 and (name N or name CA or name C or name O or name \ CB )) or resid 41 through 42 or (resid 43 and (name N or name CA or name C or na \ me O or name CB )) or resid 44 through 46 or (resid 47 and (name N or name CA or \ name C or name O or name CB )) or resid 48 through 191)) } ncs_group { reference = (chain 'E' and (resid 1 through 226 or (resid 227 and (name N or name CA or name \ C or name O or name CB )) or resid 228 through 703)) selection = (chain 'F' and (resid 1 through 247 or (resid 248 and (name N or name CA or name \ C or name O or name CB )) or resid 249 through 331 or (resid 332 and (name N or \ name CA or name C or name O or name CB )) or resid 333 through 377 or (resid 37 \ 8 through 379 and (name N or name CA or name C or name O or name CB )) or resid \ 380 through 1002)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.090 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: 0.440 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 25.890 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.170 21898 Z= 0.388 Angle : 1.147 24.482 30008 Z= 0.694 Chirality : 0.067 1.006 3465 Planarity : 0.005 0.107 3626 Dihedral : 15.247 137.102 8290 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 aren 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 covalent geometry : bond 0.00749 (21866) covalent geometry : angle 1.12580 (29980) hydrogen bonds : bond 0.18782 ( 832) hydrogen bonds : angle 8.30496 ( 2269) metal coordination : bond 0.02589 ( 32) metal coordination : angle 7.33295 ( 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 : 0.891 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: 0.8839 (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: 0.8919 (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: 0.1961 time to fit residues: 51.7702 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 : 0.918 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 88 ASN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 ASN A 492 GLN A 691 ASN A 695 ASN A 789 GLN C 31 GLN D 100 ASN D 108 ASN D 140 ASN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 281 GLN ** F 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 51 ASN E 281 GLN E 311 HIS E 361 ASN E 518 GLN E 519 ASN E 531 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.052326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.034122 restraints weight = 147546.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.035303 restraints weight = 76199.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.036087 restraints weight = 49765.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.036582 restraints weight = 37584.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.036927 restraints weight = 30992.682| |-----------------------------------------------------------------------------| r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 21898 Z= 0.241 Angle : 0.780 15.224 30008 Z= 0.399 Chirality : 0.044 0.262 3465 Planarity : 0.005 0.063 3626 Dihedral : 13.233 132.948 3684 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.92 % Favored : 89.85 % Rotamer: Outliers : 1.59 % Allowed : 13.07 % Favored : 85.34 % 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 aren not related in a simple way. whole: -3.04 (0.15), residues: 2551 helix: -0.90 (0.16), residues: 967 sheet: -1.99 (0.28), residues: 285 loop : -2.99 (0.15), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 96 TYR 0.022 0.002 TYR A 237 PHE 0.027 0.002 PHE B 15 TRP 0.023 0.002 TRP D 182 HIS 0.016 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00493 (21866) covalent geometry : angle 0.75419 (29980) hydrogen bonds : bond 0.05776 ( 832) hydrogen bonds : angle 5.74785 ( 2269) metal coordination : bond 0.01847 ( 32) metal coordination : angle 6.49612 ( 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 169 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 134 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 615 MET cc_start: 0.8499 (ptm) cc_final: 0.8210 (ppp) REVERT: A 633 MET cc_start: 0.9039 (tmm) cc_final: 0.8734 (tmm) REVERT: A 668 MET cc_start: 0.9485 (tmm) cc_final: 0.8843 (tmm) REVERT: B 49 PHE cc_start: 0.9381 (t80) cc_final: 0.9128 (m-80) REVERT: B 62 MET cc_start: 0.9348 (ppp) cc_final: 0.9034 (ppp) REVERT: B 67 MET cc_start: 0.9425 (ttm) cc_final: 0.9062 (tmm) REVERT: B 94 MET cc_start: 0.9390 (ttm) cc_final: 0.9047 (ttp) REVERT: B 142 CYS cc_start: 0.8749 (p) cc_final: 0.8059 (p) REVERT: C 21 ARG cc_start: 0.8883 (tpp80) cc_final: 0.8680 (tpp80) REVERT: D 55 MET cc_start: 0.9598 (tmm) cc_final: 0.9240 (tmm) REVERT: D 65 GLN cc_start: 0.9414 (pt0) cc_final: 0.8919 (pp30) REVERT: D 67 MET cc_start: 0.9046 (mtm) cc_final: 0.8784 (mtm) REVERT: D 88 GLN cc_start: 0.9359 (mt0) cc_final: 0.9019 (mp10) REVERT: D 90 MET cc_start: 0.9595 (ttp) cc_final: 0.9210 (ttp) REVERT: D 94 MET cc_start: 0.9002 (mtp) cc_final: 0.8770 (mtp) REVERT: F 68 MET cc_start: 0.8965 (pmm) cc_final: 0.8582 (pmm) REVERT: F 159 SER cc_start: 0.8136 (OUTLIER) cc_final: 0.7916 (p) REVERT: F 304 ILE cc_start: 0.9125 (mt) cc_final: 0.8792 (mm) REVERT: F 378 MET cc_start: 0.8867 (tpp) cc_final: 0.8233 (tpp) REVERT: E 363 LEU cc_start: 0.9492 (mt) cc_final: 0.9157 (mt) outliers start: 35 outliers final: 12 residues processed: 163 average time/residue: 0.1617 time to fit residues: 41.1576 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 : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 159 SER Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 398 TYR Chi-restraints excluded: chain F residue 455 LEU Chi-restraints excluded: chain F residue 500 LEU Chi-restraints excluded: chain F residue 561 PHE Chi-restraints excluded: chain E residue 464 HIS Chi-restraints excluded: chain E residue 479 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 1 optimal weight: 1.9990 chunk 182 optimal weight: 6.9990 chunk 144 optimal weight: 3.9990 chunk 105 optimal weight: 8.9990 chunk 82 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 94 optimal weight: 20.0000 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: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 695 ASN A 822 GLN B 140 ASN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 281 GLN ** F 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 559 ASN E 311 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.052416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.034202 restraints weight = 148128.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.035407 restraints weight = 75935.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.036185 restraints weight = 49458.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.036673 restraints weight = 37182.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.036997 restraints weight = 30826.684| |-----------------------------------------------------------------------------| r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 21898 Z= 0.205 Angle : 0.705 14.466 30008 Z= 0.362 Chirality : 0.042 0.240 3465 Planarity : 0.004 0.061 3626 Dihedral : 12.993 134.278 3681 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.23 % Favored : 89.61 % Rotamer: Outliers : 2.32 % Allowed : 14.16 % Favored : 83.52 % 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 aren not related in a simple way. whole: -2.32 (0.16), residues: 2551 helix: -0.14 (0.16), residues: 955 sheet: -1.88 (0.28), residues: 284 loop : -2.61 (0.16), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 80 TYR 0.018 0.001 TYR A 237 PHE 0.020 0.001 PHE B 15 TRP 0.018 0.001 TRP A 916 HIS 0.012 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00433 (21866) covalent geometry : angle 0.68438 (29980) hydrogen bonds : bond 0.05050 ( 832) hydrogen bonds : angle 5.25952 ( 2269) metal coordination : bond 0.01747 ( 32) metal coordination : angle 5.59694 ( 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 176 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 125 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 341 VAL cc_start: 0.9664 (OUTLIER) cc_final: 0.9379 (p) REVERT: A 370 GLU cc_start: 0.9172 (OUTLIER) cc_final: 0.8918 (pt0) REVERT: A 615 MET cc_start: 0.8437 (ptm) cc_final: 0.8191 (tmm) REVERT: A 633 MET cc_start: 0.9102 (tmm) cc_final: 0.8771 (tmm) REVERT: A 668 MET cc_start: 0.9457 (tmm) cc_final: 0.8820 (tmm) REVERT: A 902 MET cc_start: 0.8832 (ttt) cc_final: 0.8299 (tmm) REVERT: A 924 MET cc_start: 0.9677 (mmm) cc_final: 0.9233 (mmm) REVERT: B 49 PHE cc_start: 0.9413 (t80) cc_final: 0.9135 (m-80) REVERT: B 94 MET cc_start: 0.9459 (ttm) cc_final: 0.9134 (ttp) REVERT: B 158 GLN cc_start: 0.8981 (tp-100) cc_final: 0.8717 (tp-100) REVERT: D 55 MET cc_start: 0.9595 (tmm) cc_final: 0.9222 (tmm) REVERT: D 65 GLN cc_start: 0.9454 (pt0) cc_final: 0.8959 (pp30) REVERT: D 67 MET cc_start: 0.9020 (mtm) cc_final: 0.8731 (mtm) REVERT: D 70 MET cc_start: 0.9429 (tpp) cc_final: 0.8984 (tmm) REVERT: D 88 GLN cc_start: 0.9360 (mt0) cc_final: 0.9030 (mp10) REVERT: F 68 MET cc_start: 0.8928 (pmm) cc_final: 0.8506 (pmm) REVERT: F 159 SER cc_start: 0.8109 (OUTLIER) cc_final: 0.7904 (p) REVERT: F 281 GLN cc_start: 0.6191 (OUTLIER) cc_final: 0.5928 (pt0) REVERT: F 304 ILE cc_start: 0.9164 (mt) cc_final: 0.8872 (mm) REVERT: F 378 MET cc_start: 0.8872 (tpp) cc_final: 0.8150 (tpp) REVERT: F 576 MET cc_start: 0.6660 (OUTLIER) cc_final: 0.6212 (tmm) REVERT: E 363 LEU cc_start: 0.9507 (mt) cc_final: 0.9133 (mt) REVERT: E 436 MET cc_start: 0.7891 (ptp) cc_final: 0.7432 (ptm) outliers start: 51 outliers final: 23 residues processed: 168 average time/residue: 0.1510 time to fit residues: 39.5843 Evaluate side-chains 141 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 113 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 THR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 464 CYS Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain F residue 159 SER Chi-restraints excluded: chain F residue 268 ASN Chi-restraints excluded: chain F residue 281 GLN Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 455 LEU Chi-restraints excluded: chain F residue 500 LEU Chi-restraints excluded: chain F residue 510 VAL Chi-restraints excluded: chain F residue 561 PHE Chi-restraints excluded: chain F residue 576 MET Chi-restraints excluded: chain E residue 68 MET Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 401 ASP Chi-restraints excluded: chain E residue 464 HIS Chi-restraints excluded: chain E residue 479 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 125 optimal weight: 3.9990 chunk 206 optimal weight: 6.9990 chunk 162 optimal weight: 8.9990 chunk 21 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 144 optimal weight: 5.9990 chunk 205 optimal weight: 6.9990 chunk 239 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 234 optimal weight: 10.0000 chunk 182 optimal weight: 10.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 695 ASN B 19 GLN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 281 GLN ** F 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 311 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.051778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.033734 restraints weight = 148830.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.034869 restraints weight = 76656.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.035636 restraints weight = 50152.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.036138 restraints weight = 37871.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.036451 restraints weight = 31395.154| |-----------------------------------------------------------------------------| r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 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 : 0.006 0.079 21898 Z= 0.268 Angle : 0.746 14.798 30008 Z= 0.381 Chirality : 0.043 0.243 3465 Planarity : 0.005 0.061 3626 Dihedral : 12.955 135.869 3681 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.96 % Favored : 89.89 % Rotamer: Outliers : 2.77 % Allowed : 15.62 % Favored : 81.62 % 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 aren not related in a simple way. whole: -2.15 (0.16), residues: 2551 helix: -0.01 (0.16), residues: 956 sheet: -1.74 (0.27), residues: 302 loop : -2.52 (0.16), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 80 TYR 0.021 0.002 TYR A 237 PHE 0.034 0.002 PHE E 343 TRP 0.016 0.001 TRP A 916 HIS 0.013 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00566 (21866) covalent geometry : angle 0.72641 (29980) hydrogen bonds : bond 0.04967 ( 832) hydrogen bonds : angle 5.26480 ( 2269) metal coordination : bond 0.02127 ( 32) metal coordination : angle 5.56091 ( 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 181 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 120 time to evaluate : 0.876 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: 0.9169 (OUTLIER) cc_final: 0.8925 (pt0) REVERT: A 615 MET cc_start: 0.8497 (ptm) cc_final: 0.8194 (ppp) REVERT: A 633 MET cc_start: 0.9135 (tmm) cc_final: 0.8795 (tmm) REVERT: A 658 GLU cc_start: 0.8950 (tm-30) cc_final: 0.8747 (tm-30) REVERT: A 668 MET cc_start: 0.9439 (tmm) cc_final: 0.8791 (tmm) REVERT: A 902 MET cc_start: 0.8864 (ttt) cc_final: 0.8330 (tmm) REVERT: B 62 MET cc_start: 0.9376 (ppp) cc_final: 0.9047 (ppp) REVERT: B 94 MET cc_start: 0.9489 (ttm) cc_final: 0.9267 (ttp) REVERT: D 55 MET cc_start: 0.9601 (tmm) cc_final: 0.9217 (tmm) REVERT: D 65 GLN cc_start: 0.9487 (pt0) cc_final: 0.9091 (pp30) REVERT: D 67 MET cc_start: 0.9050 (mtm) cc_final: 0.8705 (mtm) REVERT: D 70 MET cc_start: 0.9432 (tpp) cc_final: 0.8986 (tmm) REVERT: D 88 GLN cc_start: 0.9368 (mt0) cc_final: 0.9041 (mp10) REVERT: F 68 MET cc_start: 0.8850 (pmm) cc_final: 0.8505 (pmm) REVERT: F 159 SER cc_start: 0.8240 (OUTLIER) cc_final: 0.8030 (p) REVERT: F 378 MET cc_start: 0.8856 (tpp) cc_final: 0.8145 (tpp) REVERT: F 429 MET cc_start: 0.9199 (tmm) cc_final: 0.8928 (tmm) REVERT: F 576 MET cc_start: 0.6590 (OUTLIER) cc_final: 0.6236 (tmm) REVERT: E 271 LYS cc_start: 0.9436 (OUTLIER) cc_final: 0.9157 (pttt) REVERT: E 363 LEU cc_start: 0.9547 (mt) cc_final: 0.9182 (mt) REVERT: E 436 MET cc_start: 0.7943 (ptp) cc_final: 0.7436 (ptp) outliers start: 61 outliers final: 33 residues processed: 171 average time/residue: 0.1611 time to fit residues: 42.4090 Evaluate side-chains 147 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 110 time to evaluate : 0.814 ------------------------------------------------------------------------------- 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 749 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 854 LEU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain 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 159 SER 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 500 LEU Chi-restraints excluded: chain F residue 510 VAL Chi-restraints excluded: chain F residue 561 PHE Chi-restraints excluded: chain F residue 576 MET Chi-restraints excluded: chain E residue 68 MET Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 271 LYS Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 401 ASP Chi-restraints excluded: chain E residue 464 HIS Chi-restraints excluded: chain E residue 479 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 153 optimal weight: 8.9990 chunk 200 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 255 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 132 optimal weight: 0.7980 chunk 245 optimal weight: 7.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 695 ASN ** B 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 ASN B 140 ASN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 281 GLN F 519 ASN F 557 ASN E 311 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.052998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.034902 restraints weight = 144781.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.036115 restraints weight = 73571.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.036875 restraints weight = 47679.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.037396 restraints weight = 36145.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.037673 restraints weight = 29763.867| |-----------------------------------------------------------------------------| r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21898 Z= 0.144 Angle : 0.662 14.607 30008 Z= 0.339 Chirality : 0.041 0.237 3465 Planarity : 0.004 0.059 3626 Dihedral : 12.811 132.296 3679 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.27 % Favored : 91.57 % Rotamer: Outliers : 2.13 % Allowed : 16.89 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.37 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.69 (0.16), residues: 2551 helix: 0.32 (0.17), residues: 964 sheet: -1.27 (0.29), residues: 278 loop : -2.29 (0.16), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 80 TYR 0.015 0.001 TYR A 237 PHE 0.023 0.001 PHE E 343 TRP 0.020 0.001 TRP A 916 HIS 0.010 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00305 (21866) covalent geometry : angle 0.64723 (29980) hydrogen bonds : bond 0.04588 ( 832) hydrogen bonds : angle 4.80237 ( 2269) metal coordination : bond 0.01362 ( 32) metal coordination : angle 4.52035 ( 28) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5102 Ramachandran restraints generated. 2551 Oldfield, 0 Emsley, 2551 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 132 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 370 GLU cc_start: 0.9183 (OUTLIER) cc_final: 0.8916 (pt0) REVERT: A 377 ASP cc_start: 0.8733 (t0) cc_final: 0.8321 (t0) REVERT: A 615 MET cc_start: 0.8439 (ptm) cc_final: 0.8044 (tmm) REVERT: A 633 MET cc_start: 0.9082 (tmm) cc_final: 0.8630 (tmm) REVERT: A 658 GLU cc_start: 0.8987 (tm-30) cc_final: 0.8728 (tm-30) REVERT: A 668 MET cc_start: 0.9408 (tmm) cc_final: 0.8778 (tmm) REVERT: A 855 MET cc_start: 0.8574 (mtm) cc_final: 0.8018 (ptp) REVERT: A 902 MET cc_start: 0.8918 (ttt) cc_final: 0.8431 (tmm) REVERT: A 924 MET cc_start: 0.9711 (mmm) cc_final: 0.9339 (mmm) REVERT: B 49 PHE cc_start: 0.9249 (t80) cc_final: 0.8963 (m-80) REVERT: B 82 LYS cc_start: 0.9367 (ptpt) cc_final: 0.9094 (ptpp) REVERT: B 94 MET cc_start: 0.9442 (ttm) cc_final: 0.9086 (ttp) REVERT: B 97 LYS cc_start: 0.9528 (pttp) cc_final: 0.9293 (pptt) REVERT: C 9 THR cc_start: 0.9376 (p) cc_final: 0.9121 (p) REVERT: C 50 GLU cc_start: 0.8827 (mt-10) cc_final: 0.8474 (mp0) REVERT: D 48 GLU cc_start: 0.9153 (pt0) cc_final: 0.8472 (tm-30) REVERT: D 55 MET cc_start: 0.9607 (tmm) cc_final: 0.9223 (tmm) REVERT: D 65 GLN cc_start: 0.9452 (pt0) cc_final: 0.9012 (pp30) REVERT: D 67 MET cc_start: 0.9052 (mtm) cc_final: 0.8749 (mtm) REVERT: D 70 MET cc_start: 0.9427 (tpp) cc_final: 0.8953 (tmm) REVERT: D 88 GLN cc_start: 0.9369 (mt0) cc_final: 0.8996 (mp10) REVERT: F 68 MET cc_start: 0.8921 (pmm) cc_final: 0.8590 (pmm) REVERT: F 295 LEU cc_start: 0.9794 (OUTLIER) cc_final: 0.9525 (mt) REVERT: F 304 ILE cc_start: 0.9185 (mt) cc_final: 0.8845 (mm) REVERT: F 378 MET cc_start: 0.8862 (tpp) cc_final: 0.8144 (tpp) REVERT: F 429 MET cc_start: 0.9147 (tmm) cc_final: 0.8919 (tmm) REVERT: F 576 MET cc_start: 0.6543 (OUTLIER) cc_final: 0.6257 (tmm) REVERT: E 363 LEU cc_start: 0.9486 (mt) cc_final: 0.9119 (mt) REVERT: E 436 MET cc_start: 0.7970 (ptp) cc_final: 0.7640 (ptp) REVERT: E 474 MET cc_start: 0.7893 (tpt) cc_final: 0.7408 (tpt) REVERT: E 561 PHE cc_start: 0.9413 (t80) cc_final: 0.9148 (t80) outliers start: 47 outliers final: 25 residues processed: 171 average time/residue: 0.1597 time to fit residues: 42.5070 Evaluate side-chains 146 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 118 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 120 THR 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 926 THR Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain F residue 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 398 TYR 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 103 VAL 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 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: 0.9990 chunk 197 optimal weight: 0.1980 chunk 18 optimal weight: 0.9980 chunk 254 optimal weight: 1.9990 chunk 130 optimal weight: 0.0010 chunk 52 optimal weight: 4.9990 chunk 202 optimal weight: 10.0000 chunk 124 optimal weight: 3.9990 chunk 217 optimal weight: 9.9990 chunk 147 optimal weight: 5.9990 chunk 250 optimal weight: 7.9990 overall best weight: 0.8390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 537 GLN E 311 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.053992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.035871 restraints weight = 143954.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.037075 restraints weight = 73404.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.037886 restraints weight = 47492.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 68)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.038394 restraints weight = 35546.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.038685 restraints weight = 29265.501| |-----------------------------------------------------------------------------| r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 21898 Z= 0.117 Angle : 0.638 14.692 30008 Z= 0.326 Chirality : 0.040 0.231 3465 Planarity : 0.004 0.058 3626 Dihedral : 12.627 130.527 3679 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.33 % Favored : 92.55 % Rotamer: Outliers : 1.77 % Allowed : 17.66 % 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 aren not related in a simple way. whole: -1.39 (0.16), residues: 2551 helix: 0.47 (0.17), residues: 968 sheet: -0.87 (0.29), residues: 282 loop : -2.10 (0.17), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 80 TYR 0.014 0.001 TYR E 476 PHE 0.024 0.001 PHE B 15 TRP 0.019 0.001 TRP A 916 HIS 0.008 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00244 (21866) covalent geometry : angle 0.62844 (29980) hydrogen bonds : bond 0.04374 ( 832) hydrogen bonds : angle 4.53765 ( 2269) metal coordination : bond 0.01204 ( 32) metal coordination : angle 3.73792 ( 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 180 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 141 time to evaluate : 0.799 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: 0.9169 (OUTLIER) cc_final: 0.8918 (pt0) REVERT: A 377 ASP cc_start: 0.8649 (t0) cc_final: 0.8305 (t0) REVERT: A 633 MET cc_start: 0.9065 (tmm) cc_final: 0.8646 (tmm) REVERT: A 658 GLU cc_start: 0.8952 (tm-30) cc_final: 0.8735 (tm-30) REVERT: A 668 MET cc_start: 0.9335 (tmm) cc_final: 0.8718 (tmm) REVERT: A 855 MET cc_start: 0.8566 (mtm) cc_final: 0.8008 (ptp) REVERT: A 865 ASP cc_start: 0.9216 (m-30) cc_final: 0.8994 (m-30) REVERT: A 902 MET cc_start: 0.8898 (ttt) cc_final: 0.8240 (tmm) REVERT: A 924 MET cc_start: 0.9686 (mmm) cc_final: 0.9182 (mmm) REVERT: B 49 PHE cc_start: 0.9214 (t80) cc_final: 0.8924 (m-80) REVERT: B 82 LYS cc_start: 0.9363 (ptpt) cc_final: 0.9068 (pttm) REVERT: B 94 MET cc_start: 0.9379 (ttm) cc_final: 0.9094 (ttp) REVERT: C 9 THR cc_start: 0.9111 (p) cc_final: 0.8388 (p) REVERT: D 55 MET cc_start: 0.9610 (tmm) cc_final: 0.9228 (tmm) REVERT: D 65 GLN cc_start: 0.9427 (pt0) cc_final: 0.9021 (pp30) REVERT: D 67 MET cc_start: 0.9079 (mtm) cc_final: 0.8611 (mtm) REVERT: D 70 MET cc_start: 0.9435 (tpp) cc_final: 0.8992 (tmm) REVERT: D 88 GLN cc_start: 0.9430 (mt0) cc_final: 0.9058 (mp10) REVERT: D 90 MET cc_start: 0.9574 (ttp) cc_final: 0.9221 (tmm) REVERT: F 68 MET cc_start: 0.8908 (pmm) cc_final: 0.8574 (pmm) REVERT: F 295 LEU cc_start: 0.9801 (OUTLIER) cc_final: 0.9529 (mt) REVERT: F 304 ILE cc_start: 0.9140 (mt) cc_final: 0.8784 (mm) REVERT: F 378 MET cc_start: 0.8894 (tpp) cc_final: 0.8191 (tpp) REVERT: F 429 MET cc_start: 0.9176 (tmm) cc_final: 0.8949 (tmm) REVERT: F 576 MET cc_start: 0.6725 (OUTLIER) cc_final: 0.6387 (tmm) REVERT: E 68 MET cc_start: 0.1875 (tpt) cc_final: 0.1582 (tpt) REVERT: E 274 MET cc_start: 0.9074 (tpt) cc_final: 0.8171 (tpp) REVERT: E 295 LEU cc_start: 0.9870 (tp) cc_final: 0.9527 (pp) REVERT: E 363 LEU cc_start: 0.9453 (mt) cc_final: 0.9074 (mt) REVERT: E 436 MET cc_start: 0.7906 (ptp) cc_final: 0.7539 (ptp) REVERT: E 474 MET cc_start: 0.7469 (tpt) cc_final: 0.6963 (tpt) outliers start: 39 outliers final: 22 residues processed: 175 average time/residue: 0.1702 time to fit residues: 46.0697 Evaluate side-chains 147 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 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 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 444 CYS Chi-restraints excluded: chain F residue 500 LEU Chi-restraints excluded: chain F residue 510 VAL Chi-restraints excluded: chain F residue 576 MET Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 340 VAL 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: 6.9990 chunk 22 optimal weight: 4.9990 chunk 158 optimal weight: 7.9990 chunk 211 optimal weight: 2.9990 chunk 194 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 227 optimal weight: 8.9990 chunk 3 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 88 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 554 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 = 0.3388 r_free = 0.3388 target = 0.051848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.034844 restraints weight = 149875.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.035785 restraints weight = 82819.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.036176 restraints weight = 47256.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.036367 restraints weight = 38575.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.036396 restraints weight = 34369.774| |-----------------------------------------------------------------------------| r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 21898 Z= 0.303 Angle : 0.770 14.501 30008 Z= 0.391 Chirality : 0.043 0.243 3465 Planarity : 0.005 0.056 3626 Dihedral : 12.743 136.507 3679 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.49 % Favored : 90.40 % Rotamer: Outliers : 2.50 % Allowed : 18.16 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.37 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.62 (0.16), residues: 2551 helix: 0.32 (0.17), residues: 967 sheet: -1.25 (0.29), residues: 280 loop : -2.20 (0.16), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG F 178 TYR 0.025 0.002 TYR A 237 PHE 0.026 0.002 PHE A 753 TRP 0.011 0.002 TRP A 916 HIS 0.012 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00636 (21866) covalent geometry : angle 0.75467 (29980) hydrogen bonds : bond 0.04759 ( 832) hydrogen bonds : angle 4.95596 ( 2269) metal coordination : bond 0.02420 ( 32) metal coordination : angle 4.98741 ( 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 174 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 119 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 370 GLU cc_start: 0.9187 (OUTLIER) cc_final: 0.8946 (pt0) REVERT: A 633 MET cc_start: 0.9173 (tmm) cc_final: 0.8712 (tmm) REVERT: A 658 GLU cc_start: 0.9033 (tm-30) cc_final: 0.8770 (tm-30) REVERT: A 668 MET cc_start: 0.9387 (tmm) cc_final: 0.8694 (tmm) REVERT: A 924 MET cc_start: 0.9662 (mmm) cc_final: 0.9093 (mmm) REVERT: B 49 PHE cc_start: 0.9200 (t80) cc_final: 0.8911 (m-80) REVERT: B 82 LYS cc_start: 0.9377 (ptpt) cc_final: 0.9149 (ptpp) REVERT: B 94 MET cc_start: 0.9516 (ttm) cc_final: 0.9308 (ttp) REVERT: C 9 THR cc_start: 0.8970 (p) cc_final: 0.8568 (p) REVERT: C 52 MET cc_start: 0.9199 (tpt) cc_final: 0.8934 (ttt) REVERT: D 55 MET cc_start: 0.9602 (tmm) cc_final: 0.9206 (tmm) REVERT: D 65 GLN cc_start: 0.9451 (pt0) cc_final: 0.9029 (pp30) REVERT: D 67 MET cc_start: 0.9107 (mtm) cc_final: 0.8866 (mtm) REVERT: D 88 GLN cc_start: 0.9494 (mt0) cc_final: 0.9177 (mp10) REVERT: D 90 MET cc_start: 0.9599 (ttp) cc_final: 0.9257 (tmm) REVERT: D 182 TRP cc_start: 0.8500 (OUTLIER) cc_final: 0.7802 (m100) REVERT: F 68 MET cc_start: 0.9009 (pmm) cc_final: 0.8631 (pmm) REVERT: F 295 LEU cc_start: 0.9806 (OUTLIER) cc_final: 0.9550 (mt) REVERT: F 304 ILE cc_start: 0.9214 (mt) cc_final: 0.8889 (mm) REVERT: F 378 MET cc_start: 0.8843 (tpp) cc_final: 0.8137 (tpp) REVERT: F 576 MET cc_start: 0.6895 (OUTLIER) cc_final: 0.6551 (tmm) REVERT: E 363 LEU cc_start: 0.9584 (mt) cc_final: 0.9205 (mt) REVERT: E 435 ASP cc_start: 0.8817 (OUTLIER) cc_final: 0.8610 (p0) REVERT: E 436 MET cc_start: 0.7984 (ptp) cc_final: 0.7598 (ptp) REVERT: E 474 MET cc_start: 0.7874 (tpt) cc_final: 0.7363 (tpt) outliers start: 55 outliers final: 35 residues processed: 166 average time/residue: 0.1697 time to fit residues: 43.7340 Evaluate side-chains 150 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 110 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 393 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 905 VAL Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 89 VAL 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 500 LEU Chi-restraints excluded: chain F residue 510 VAL Chi-restraints excluded: chain F residue 561 PHE Chi-restraints excluded: chain F residue 576 MET Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 318 CYS Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 401 ASP Chi-restraints excluded: chain E residue 435 ASP Chi-restraints excluded: chain E residue 464 HIS Chi-restraints excluded: chain E residue 479 VAL Chi-restraints excluded: chain E residue 531 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 140 optimal weight: 4.9990 chunk 94 optimal weight: 20.0000 chunk 120 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 101 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 171 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 GLN ** B 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 GLN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 311 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.052731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.034773 restraints weight = 145154.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.035929 restraints weight = 74057.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.036715 restraints weight = 48151.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.037229 restraints weight = 36192.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.037502 restraints weight = 29897.213| |-----------------------------------------------------------------------------| r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21898 Z= 0.157 Angle : 0.682 14.965 30008 Z= 0.345 Chirality : 0.041 0.236 3465 Planarity : 0.004 0.059 3626 Dihedral : 12.737 133.023 3679 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.80 % Favored : 92.08 % Rotamer: Outliers : 2.32 % Allowed : 18.66 % Favored : 79.03 % 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 aren not related in a simple way. whole: -1.39 (0.16), residues: 2551 helix: 0.52 (0.17), residues: 967 sheet: -1.08 (0.30), residues: 274 loop : -2.07 (0.17), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 80 TYR 0.015 0.001 TYR A 237 PHE 0.026 0.001 PHE D 92 TRP 0.017 0.001 TRP A 916 HIS 0.007 0.001 HIS A 892 Details of bonding type rmsd covalent geometry : bond 0.00336 (21866) covalent geometry : angle 0.67067 (29980) hydrogen bonds : bond 0.04449 ( 832) hydrogen bonds : angle 4.68440 ( 2269) metal coordination : bond 0.01425 ( 32) metal coordination : angle 4.19336 ( 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 167 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 116 time to evaluate : 0.854 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: 0.9248 (mmm) cc_final: 0.8962 (mmm) REVERT: A 370 GLU cc_start: 0.9155 (OUTLIER) cc_final: 0.8892 (pt0) REVERT: A 633 MET cc_start: 0.9067 (tmm) cc_final: 0.8707 (tmm) REVERT: A 658 GLU cc_start: 0.8952 (tm-30) cc_final: 0.8664 (tm-30) REVERT: A 668 MET cc_start: 0.9365 (tmm) cc_final: 0.8717 (tmm) REVERT: A 902 MET cc_start: 0.8832 (ttt) cc_final: 0.8104 (tmm) REVERT: A 924 MET cc_start: 0.9664 (mmm) cc_final: 0.9131 (mmm) REVERT: B 49 PHE cc_start: 0.9190 (t80) cc_final: 0.8902 (m-80) REVERT: B 62 MET cc_start: 0.9325 (ppp) cc_final: 0.9076 (ppp) REVERT: B 82 LYS cc_start: 0.9373 (ptpt) cc_final: 0.9090 (ptpp) REVERT: B 94 MET cc_start: 0.9387 (ttm) cc_final: 0.9089 (ttp) REVERT: C 3 MET cc_start: 0.8727 (mmp) cc_final: 0.8516 (mmt) REVERT: C 9 THR cc_start: 0.8944 (p) cc_final: 0.8481 (p) REVERT: C 52 MET cc_start: 0.9181 (tpt) cc_final: 0.8909 (ttt) REVERT: D 55 MET cc_start: 0.9591 (tmm) cc_final: 0.9201 (tmm) REVERT: D 65 GLN cc_start: 0.9418 (pt0) cc_final: 0.8981 (pp30) REVERT: D 67 MET cc_start: 0.9033 (mtm) cc_final: 0.8688 (mtm) REVERT: D 70 MET cc_start: 0.9351 (tpp) cc_final: 0.8991 (tmm) REVERT: D 88 GLN cc_start: 0.9480 (mt0) cc_final: 0.9084 (mp10) REVERT: D 90 MET cc_start: 0.9557 (ttp) cc_final: 0.9259 (tmm) REVERT: F 68 MET cc_start: 0.8836 (pmm) cc_final: 0.8479 (pmm) REVERT: F 295 LEU cc_start: 0.9807 (OUTLIER) cc_final: 0.9515 (mt) REVERT: F 304 ILE cc_start: 0.9201 (mt) cc_final: 0.8859 (mm) REVERT: F 378 MET cc_start: 0.8884 (tpp) cc_final: 0.8171 (tpp) REVERT: F 576 MET cc_start: 0.6784 (OUTLIER) cc_final: 0.6522 (tmm) REVERT: E 363 LEU cc_start: 0.9523 (mt) cc_final: 0.9140 (mt) REVERT: E 474 MET cc_start: 0.7583 (tpt) cc_final: 0.7029 (tpt) outliers start: 51 outliers final: 35 residues processed: 160 average time/residue: 0.1654 time to fit residues: 41.4246 Evaluate side-chains 150 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 112 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 ILE 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 786 LEU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 89 VAL 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 510 VAL Chi-restraints excluded: chain F residue 561 PHE Chi-restraints excluded: chain F residue 576 MET Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 183 THR 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 479 VAL Chi-restraints excluded: chain E residue 531 GLN Chi-restraints excluded: chain E residue 573 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 77 optimal weight: 8.9990 chunk 103 optimal weight: 0.5980 chunk 135 optimal weight: 10.0000 chunk 152 optimal weight: 8.9990 chunk 247 optimal weight: 0.0570 chunk 42 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 chunk 68 optimal weight: 6.9990 chunk 121 optimal weight: 9.9990 chunk 138 optimal weight: 10.0000 chunk 186 optimal weight: 7.9990 overall best weight: 2.1304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** E 311 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.052835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.034960 restraints weight = 143777.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.036110 restraints weight = 73553.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.036879 restraints weight = 47531.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.037379 restraints weight = 35771.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.037672 restraints weight = 29637.594| |-----------------------------------------------------------------------------| r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21898 Z= 0.157 Angle : 0.669 14.876 30008 Z= 0.337 Chirality : 0.041 0.233 3465 Planarity : 0.004 0.058 3626 Dihedral : 12.653 132.856 3679 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.39 % Favored : 91.53 % Rotamer: Outliers : 2.22 % Allowed : 18.57 % Favored : 79.21 % 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 aren not related in a simple way. whole: -1.23 (0.17), residues: 2551 helix: 0.63 (0.17), residues: 971 sheet: -0.81 (0.31), residues: 270 loop : -2.01 (0.17), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 80 TYR 0.015 0.001 TYR A 237 PHE 0.020 0.001 PHE E 343 TRP 0.017 0.001 TRP A 916 HIS 0.007 0.001 HIS A 892 Details of bonding type rmsd covalent geometry : bond 0.00337 (21866) covalent geometry : angle 0.65882 (29980) hydrogen bonds : bond 0.04313 ( 832) hydrogen bonds : angle 4.58038 ( 2269) metal coordination : bond 0.01417 ( 32) metal coordination : angle 3.94781 ( 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 164 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 115 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: symmetry clash revert: symmetry clash REVERT: A 370 GLU cc_start: 0.9150 (OUTLIER) cc_final: 0.8893 (pt0) REVERT: A 633 MET cc_start: 0.9050 (tmm) cc_final: 0.8593 (tmm) REVERT: A 658 GLU cc_start: 0.8960 (tm-30) cc_final: 0.8668 (tm-30) REVERT: A 668 MET cc_start: 0.9340 (tmm) cc_final: 0.8676 (tmm) REVERT: A 902 MET cc_start: 0.8825 (ttt) cc_final: 0.8153 (tmm) REVERT: A 924 MET cc_start: 0.9678 (mmm) cc_final: 0.9116 (mmm) REVERT: B 49 PHE cc_start: 0.9196 (t80) cc_final: 0.8908 (m-80) REVERT: B 62 MET cc_start: 0.9305 (ppp) cc_final: 0.9063 (ppp) REVERT: B 94 MET cc_start: 0.9405 (ttm) cc_final: 0.9076 (ttp) REVERT: C 9 THR cc_start: 0.8957 (p) cc_final: 0.8424 (p) REVERT: C 52 MET cc_start: 0.9204 (tpt) cc_final: 0.8907 (ttt) REVERT: D 55 MET cc_start: 0.9602 (tmm) cc_final: 0.9215 (tmm) REVERT: D 65 GLN cc_start: 0.9407 (pt0) cc_final: 0.8998 (pp30) REVERT: D 67 MET cc_start: 0.9068 (mtm) cc_final: 0.8703 (mtm) REVERT: D 70 MET cc_start: 0.9359 (tpp) cc_final: 0.8990 (tmm) REVERT: D 90 MET cc_start: 0.9561 (ttp) cc_final: 0.9293 (tmm) REVERT: D 182 TRP cc_start: 0.8404 (OUTLIER) cc_final: 0.7688 (m100) REVERT: F 68 MET cc_start: 0.8857 (pmm) cc_final: 0.8490 (pmm) REVERT: F 295 LEU cc_start: 0.9811 (OUTLIER) cc_final: 0.9530 (mt) REVERT: F 304 ILE cc_start: 0.9198 (mt) cc_final: 0.8864 (mm) REVERT: F 378 MET cc_start: 0.8897 (tpp) cc_final: 0.8171 (tpp) REVERT: F 576 MET cc_start: 0.6837 (OUTLIER) cc_final: 0.6583 (tmm) REVERT: E 68 MET cc_start: 0.0478 (tpt) cc_final: 0.0163 (tpt) REVERT: E 363 LEU cc_start: 0.9533 (mt) cc_final: 0.9128 (mt) REVERT: E 436 MET cc_start: 0.8009 (ptp) cc_final: 0.7726 (ptp) REVERT: E 474 MET cc_start: 0.7445 (tpt) cc_final: 0.6796 (tpt) outliers start: 49 outliers final: 37 residues processed: 157 average time/residue: 0.1572 time to fit residues: 38.7102 Evaluate side-chains 154 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 113 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 393 THR 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 786 LEU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 89 VAL 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 500 LEU Chi-restraints excluded: chain F residue 510 VAL Chi-restraints excluded: chain F residue 561 PHE Chi-restraints excluded: chain F residue 576 MET Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 183 THR 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 435 ASP Chi-restraints excluded: chain E residue 464 HIS Chi-restraints excluded: chain E residue 479 VAL Chi-restraints excluded: chain E residue 531 GLN Chi-restraints excluded: chain E residue 573 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 247 optimal weight: 0.0470 chunk 10 optimal weight: 8.9990 chunk 181 optimal weight: 0.8980 chunk 79 optimal weight: 0.5980 chunk 162 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 211 optimal weight: 3.9990 chunk 246 optimal weight: 6.9990 chunk 206 optimal weight: 0.9990 chunk 109 optimal weight: 4.9990 chunk 173 optimal weight: 1.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 81 GLN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 GLN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 311 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.053733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.035745 restraints weight = 143153.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.036928 restraints weight = 73161.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.037724 restraints weight = 47815.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.038236 restraints weight = 35802.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.038589 restraints weight = 29559.788| |-----------------------------------------------------------------------------| r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 21898 Z= 0.116 Angle : 0.661 15.042 30008 Z= 0.331 Chirality : 0.040 0.228 3465 Planarity : 0.004 0.059 3626 Dihedral : 12.597 130.171 3679 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.51 % Favored : 93.41 % Rotamer: Outliers : 1.36 % Allowed : 19.34 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.98 % Cis-general : 0.37 % Twisted Proline : 0.98 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.11 (0.17), residues: 2551 helix: 0.67 (0.17), residues: 976 sheet: -0.68 (0.31), residues: 264 loop : -1.91 (0.17), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 80 TYR 0.011 0.001 TYR B 71 PHE 0.020 0.001 PHE E 343 TRP 0.024 0.001 TRP B 182 HIS 0.007 0.001 HIS A 892 Details of bonding type rmsd covalent geometry : bond 0.00246 (21866) covalent geometry : angle 0.65254 (29980) hydrogen bonds : bond 0.04315 ( 832) hydrogen bonds : angle 4.43979 ( 2269) metal coordination : bond 0.01208 ( 32) metal coordination : angle 3.53045 ( 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 159 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 129 time to evaluate : 0.906 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: 0.9255 (mmm) cc_final: 0.8954 (mmm) REVERT: A 370 GLU cc_start: 0.9152 (OUTLIER) cc_final: 0.8898 (pt0) REVERT: A 633 MET cc_start: 0.8996 (tmm) cc_final: 0.8591 (tmm) REVERT: A 658 GLU cc_start: 0.8966 (tm-30) cc_final: 0.8666 (tm-30) REVERT: A 668 MET cc_start: 0.9310 (tmm) cc_final: 0.8676 (tmm) REVERT: A 902 MET cc_start: 0.8770 (ttt) cc_final: 0.8122 (tmm) REVERT: A 924 MET cc_start: 0.9691 (mmm) cc_final: 0.9121 (mmm) REVERT: B 49 PHE cc_start: 0.9181 (t80) cc_final: 0.8887 (m-80) REVERT: B 62 MET cc_start: 0.9329 (ppp) cc_final: 0.9010 (ppp) REVERT: B 82 LYS cc_start: 0.9368 (ptpt) cc_final: 0.9138 (ptpp) REVERT: B 158 GLN cc_start: 0.9031 (tp-100) cc_final: 0.8754 (tp-100) REVERT: C 9 THR cc_start: 0.8916 (p) cc_final: 0.8288 (p) REVERT: C 52 MET cc_start: 0.9171 (tpt) cc_final: 0.8879 (ttt) REVERT: D 55 MET cc_start: 0.9608 (tmm) cc_final: 0.9225 (tmm) REVERT: D 65 GLN cc_start: 0.9377 (pt0) cc_final: 0.9003 (pp30) REVERT: D 67 MET cc_start: 0.9089 (mtm) cc_final: 0.8661 (mtm) REVERT: D 70 MET cc_start: 0.9345 (tpp) cc_final: 0.8973 (tmm) REVERT: D 88 GLN cc_start: 0.9376 (mt0) cc_final: 0.9080 (mp10) REVERT: D 90 MET cc_start: 0.9539 (ttp) cc_final: 0.9321 (tmm) REVERT: D 182 TRP cc_start: 0.8324 (OUTLIER) cc_final: 0.7585 (m100) REVERT: F 68 MET cc_start: 0.8839 (pmm) cc_final: 0.8498 (pmm) REVERT: F 295 LEU cc_start: 0.9803 (tp) cc_final: 0.9514 (mt) REVERT: F 304 ILE cc_start: 0.9180 (mt) cc_final: 0.8840 (mm) REVERT: F 373 PHE cc_start: 0.9140 (t80) cc_final: 0.8847 (t80) REVERT: F 378 MET cc_start: 0.8940 (tpp) cc_final: 0.8250 (tpp) REVERT: F 429 MET cc_start: 0.9503 (tmm) cc_final: 0.8674 (ppp) REVERT: F 576 MET cc_start: 0.6833 (OUTLIER) cc_final: 0.6607 (tmm) REVERT: E 68 MET cc_start: 0.0448 (tpt) cc_final: 0.0119 (tpt) REVERT: E 363 LEU cc_start: 0.9452 (mt) cc_final: 0.9080 (mt) REVERT: E 436 MET cc_start: 0.8019 (ptp) cc_final: 0.7706 (ptp) REVERT: E 474 MET cc_start: 0.7498 (tpt) cc_final: 0.6960 (tpt) outliers start: 30 outliers final: 25 residues processed: 156 average time/residue: 0.1617 time to fit residues: 39.1529 Evaluate side-chains 145 residues out of total 2240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 117 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 160 VAL Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 268 ASN Chi-restraints excluded: chain F residue 332 ARG Chi-restraints excluded: chain F residue 444 CYS Chi-restraints excluded: chain F residue 500 LEU Chi-restraints excluded: chain F residue 510 VAL Chi-restraints excluded: chain F residue 576 MET Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 318 CYS Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 435 ASP Chi-restraints excluded: chain E residue 464 HIS Chi-restraints excluded: chain E residue 479 VAL 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 107 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 183 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 249 optimal weight: 1.9990 chunk 192 optimal weight: 3.9990 chunk 142 optimal weight: 10.0000 chunk 204 optimal weight: 6.9990 chunk 193 optimal weight: 7.9990 chunk 141 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 886 GLN B 56 GLN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 311 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.052555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.034721 restraints weight = 145355.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.035869 restraints weight = 74174.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.036603 restraints weight = 47959.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.037103 restraints weight = 36250.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.037414 restraints weight = 29968.304| |-----------------------------------------------------------------------------| r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21898 Z= 0.191 Angle : 0.697 15.035 30008 Z= 0.351 Chirality : 0.041 0.233 3465 Planarity : 0.004 0.057 3626 Dihedral : 12.592 133.275 3679 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.39 % Favored : 91.53 % Rotamer: Outliers : 1.86 % Allowed : 19.11 % Favored : 79.03 % 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 aren not related in a simple way. whole: -1.18 (0.17), residues: 2551 helix: 0.63 (0.17), residues: 977 sheet: -0.82 (0.30), residues: 279 loop : -1.95 (0.17), residues: 1295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 80 TYR 0.020 0.001 TYR E 476 PHE 0.044 0.002 PHE B 147 TRP 0.015 0.001 TRP B 154 HIS 0.006 0.001 HIS A 892 Details of bonding type rmsd covalent geometry : bond 0.00408 (21866) covalent geometry : angle 0.68686 (29980) hydrogen bonds : bond 0.04306 ( 832) hydrogen bonds : angle 4.60414 ( 2269) metal coordination : bond 0.01606 ( 32) metal coordination : angle 3.95917 ( 28) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4541.06 seconds wall clock time: 79 minutes 13.57 seconds (4753.57 seconds total)