Starting phenix.real_space_refine on Fri Aug 7 14:13:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8gwn_34317/08_2026/8gwn_34317.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gwn_34317/08_2026/8gwn_34317.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8gwn_34317/08_2026/8gwn_34317.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gwn_34317/08_2026/8gwn_34317.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8gwn_34317/08_2026/8gwn_34317.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8gwn_34317/08_2026/8gwn_34317.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gwn_34317/08_2026/8gwn_34317.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gwn_34317/08_2026/8gwn_34317.map" } resolution = 3.38 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= 0.031 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 55 5.49 5 S 157 5.16 5 C 13680 2.51 5 N 3680 2.21 5 O 4280 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 180 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21860 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 926, 7458 Classifications: {'peptide': 926} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 895} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 1396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1396 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 6, 'TRANS': 180} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'TYR:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "C" Number of atoms: 553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 553 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Chain: "D" Number of atoms: 1414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1414 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 179} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "I" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 545 Classifications: {'RNAv2': 25} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 16, 'rna3p_pyr': 8} Link IDs: {'rna3p': 24} Chain: "J" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 565 Classifications: {'RNAv2': 27} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 9, 'rna3p_pyr': 17} Link IDs: {'rna2p': 1, 'rna3p': 25} Chain: "F" Number of atoms: 4508 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 585, 4500 Classifications: {'peptide': 585} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 554} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 5, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 35 Conformer: "B" Number of residues, atoms: 585, 4500 Classifications: {'peptide': 585} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 554} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 5, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 35 bond proxies already assigned to first conformer: 4593 Chain: "E" Number of atoms: 4513 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 586, 4505 Classifications: {'peptide': 586} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 555} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 5, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 35 Conformer: "B" Number of residues, atoms: 586, 4505 Classifications: {'peptide': 586} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 555} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 5, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 35 bond proxies already assigned to first conformer: 4598 Chain: "G" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 868 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {' ZN': 2, 'GNP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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 74.280 54.942 120.937 1.00 61.03 S ATOM 2487 SG CYS A 306 74.416 55.990 124.470 1.00 52.01 S ATOM 2519 SG CYS A 310 75.733 52.495 123.381 1.00 54.62 S ATOM 3927 SG CYS A 487 76.596 68.467 104.297 1.00 81.63 S ATOM 5180 SG CYS A 645 76.072 70.276 107.632 1.00 97.07 S ATOM 5186 SG CYS A 646 74.444 67.003 107.129 1.00 93.93 S ATOM 12035 SG CYS F 16 102.069 64.263 49.138 1.00184.25 S ATOM 12050 SG CYS F 19 102.611 61.058 47.444 1.00216.23 S ATOM 11953 SG CYS F 5 114.775 65.599 50.631 1.00195.56 S ATOM 11974 SG CYS F 8 115.770 67.865 48.306 1.00207.32 S ATOM 12112 SG CYS F 26 113.677 69.268 51.082 1.00170.90 S ATOM 12129 SG CYS F 29 112.210 67.456 47.985 1.00173.45 S ATOM 12294 SG CYS F 50 91.661 75.350 63.482 1.00170.32 S ATOM 12324 SG CYS F 55 88.824 73.752 61.593 1.00174.05 S ATOM 12457 SG CYS F 72 89.998 77.327 60.561 1.00173.25 S ATOM 16548 SG CYS E 16 59.780 73.270 64.162 1.00158.57 S ATOM 16563 SG CYS E 19 57.247 70.438 63.668 1.00176.05 S ATOM 16466 SG CYS E 5 69.445 69.147 57.445 1.00167.73 S ATOM 16487 SG CYS E 8 68.770 71.370 54.348 1.00188.38 S ATOM 16625 SG CYS E 26 70.633 73.072 57.176 1.00171.23 S ATOM 16642 SG CYS E 29 67.187 72.462 57.046 1.00180.75 S ATOM 16807 SG CYS E 50 65.123 86.919 78.331 1.00196.86 S ATOM 16837 SG CYS E 55 61.510 87.331 79.191 1.00214.41 S ATOM 16970 SG CYS E 72 62.922 88.544 75.859 1.00205.06 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AMET F 474 " occ=0.41 ... (14 atoms not shown) pdb=" CE BMET F 474 " occ=0.59 residue: pdb=" N AMET E 474 " occ=0.41 ... (14 atoms not shown) pdb=" CE BMET E 474 " occ=0.59 Time building chain proxies: 6.34, per 1000 atoms: 0.29 Number of scatterers: 21860 At special positions: 0 Unit cell: (154.16, 135.3, 182.86, 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 157 16.00 P 55 15.00 O 4280 8.00 N 3680 7.00 C 13680 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.54 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb=" ZN E 701 " pdb="ZN ZN E 701 " - pdb=" ND1 HIS E 39 " pdb="ZN ZN E 701 " - pdb=" NE2 HIS E 33 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 16 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 19 " pdb=" ZN E 702 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 8 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 29 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 26 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 5 " pdb=" ZN E 703 " pdb="ZN ZN E 703 " - pdb=" NE2 HIS E 75 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 50 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 55 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 72 " pdb=" ZN F 701 " pdb="ZN ZN F 701 " - pdb=" ND1 HIS F 39 " pdb="ZN ZN F 701 " - pdb=" NE2 HIS F 33 " pdb="ZN ZN F 701 " - pdb=" SG CYS F 19 " pdb="ZN ZN F 701 " - pdb=" SG CYS F 16 " pdb=" ZN F 702 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 8 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 26 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 5 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 29 " pdb=" ZN F 703 " pdb="ZN ZN F 703 " - pdb=" ND1 HIS F 75 " pdb="ZN ZN F 703 " - pdb=" SG CYS F 55 " pdb="ZN ZN F 703 " - pdb=" SG CYS F 72 " pdb="ZN ZN F 703 " - pdb=" SG CYS F 50 " Number of angles added : 28 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5068 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 27 sheets defined 38.1% alpha, 6.3% beta 14 base pairs and 35 stacking pairs defined. Time for finding SS restraints: 3.58 Creating SS restraints... Processing helix chain 'A' and resid 5 through 12 removed outlier: 3.783A pdb=" N ASN A 9 " --> pdb=" O GLN A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 64 removed outlier: 4.041A pdb=" N ASN A 64 " --> pdb=" O GLU A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 91 removed outlier: 3.754A pdb=" N GLN A 81 " --> pdb=" O PHE A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 133 removed outlier: 4.070A pdb=" N LEU A 127 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 149 removed outlier: 3.695A pdb=" N TYR A 149 " --> pdb=" O ILE A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 158 Processing helix chain 'A' and resid 170 through 176 Processing helix chain 'A' and resid 178 through 200 Processing helix chain 'A' and resid 235 through 242 Processing helix chain 'A' and resid 243 through 247 removed outlier: 3.733A pdb=" N THR A 246 " --> pdb=" O PRO A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 255 Processing helix chain 'A' and resid 277 through 286 Processing helix chain 'A' and resid 297 through 301 removed outlier: 3.639A pdb=" N ASN A 300 " --> pdb=" O ASN A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 317 removed outlier: 4.727A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 376 Processing helix chain 'A' and resid 377 through 384 removed outlier: 4.341A pdb=" N HIS A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 426 removed outlier: 3.828A pdb=" N LYS A 426 " --> pdb=" O PHE A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 454 Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 468 through 480 removed outlier: 5.683A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 509 removed outlier: 3.590A pdb=" N LYS A 508 " --> pdb=" O PRO A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 518 removed outlier: 3.998A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 529 removed outlier: 3.530A pdb=" N GLN A 524 " --> pdb=" O SER A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 580 removed outlier: 3.905A pdb=" N THR A 565 " --> pdb=" O SER A 561 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 606 removed outlier: 4.016A pdb=" N TYR A 606 " --> pdb=" O LEU A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 639 removed outlier: 3.888A pdb=" N ARG A 631 " --> pdb=" O PRO A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 663 removed outlier: 3.737A pdb=" N LEU A 663 " --> pdb=" O CYS A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 709 removed outlier: 4.083A pdb=" N SER A 692 " --> pdb=" O ALA A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 732 Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 779 through 791 Processing helix chain 'A' and resid 833 through 842 Processing helix chain 'A' and resid 852 through 854 No H-bonds generated for 'chain 'A' and resid 852 through 854' Processing helix chain 'A' and resid 855 through 866 removed outlier: 4.282A pdb=" N PHE A 859 " --> pdb=" O MET A 855 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL A 860 " --> pdb=" O ILE A 856 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N SER A 861 " --> pdb=" O GLU A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 903 removed outlier: 4.338A pdb=" N ALA A 878 " --> pdb=" O ASN A 874 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP A 879 " --> pdb=" O GLN A 875 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLY A 897 " --> pdb=" O ASP A 893 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N MET A 902 " --> pdb=" O HIS A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 922 removed outlier: 4.344A pdb=" N TYR A 921 " --> pdb=" O GLU A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 926 Processing helix chain 'B' and resid 11 through 29 Processing helix chain 'B' and resid 32 through 50 removed outlier: 3.564A pdb=" N LEU B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN B 43 " --> pdb=" O LYS B 39 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N SER B 47 " --> pdb=" O ASN B 43 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHE B 49 " --> pdb=" O ALA B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 95 removed outlier: 4.724A pdb=" N ARG B 57 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LYS B 58 " --> pdb=" O ALA B 54 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS B 61 " --> pdb=" O ARG B 57 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA B 81 " --> pdb=" O GLU B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 108 Processing helix chain 'B' and resid 116 through 118 No H-bonds generated for 'chain 'B' and resid 116 through 118' Processing helix chain 'B' and resid 119 through 125 Processing helix chain 'B' and resid 134 through 140 removed outlier: 4.021A pdb=" N ASN B 140 " --> pdb=" O ASN B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 180 removed outlier: 3.733A pdb=" N ASN B 179 " --> pdb=" O ASN B 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 19 Processing helix chain 'C' and resid 26 through 40 removed outlier: 3.988A pdb=" N LEU C 40 " --> pdb=" O HIS C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 61 removed outlier: 3.508A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 71 Processing helix chain 'D' and resid 9 through 29 Processing helix chain 'D' and resid 31 through 38 removed outlier: 4.254A pdb=" N LEU D 35 " --> pdb=" O SER D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 50 Processing helix chain 'D' and resid 51 through 80 removed outlier: 4.594A pdb=" N ARG D 57 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS D 61 " --> pdb=" O ARG D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 99 removed outlier: 4.494A pdb=" N GLN D 88 " --> pdb=" O THR D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 134 through 141 removed outlier: 3.707A pdb=" N TYR D 138 " --> pdb=" O ASP D 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 35 Processing helix chain 'F' and resid 103 through 111 Processing helix chain 'F' and resid 116 through 124 Processing helix chain 'F' and resid 127 through 147 Processing helix chain 'F' and resid 265 through 273 removed outlier: 5.289A pdb=" N LYS F 271 " --> pdb=" O ALA F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 290 through 299 removed outlier: 3.824A pdb=" N LEU F 297 " --> pdb=" O ILE F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 325 removed outlier: 4.234A pdb=" N ALA F 316 " --> pdb=" O ALA F 312 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N LEU F 317 " --> pdb=" O ALA F 313 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS F 320 " --> pdb=" O ALA F 316 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU F 322 " --> pdb=" O CYS F 318 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS F 323 " --> pdb=" O GLU F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 391 removed outlier: 3.677A pdb=" N LEU F 384 " --> pdb=" O THR F 380 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL F 387 " --> pdb=" O ASP F 383 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASN F 388 " --> pdb=" O LEU F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 418 through 422 Processing helix chain 'F' and resid 423 through 432 removed outlier: 3.840A pdb=" N ARG F 427 " --> pdb=" O ASN F 423 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU F 428 " --> pdb=" O SER F 424 " (cutoff:3.500A) Processing helix chain 'F' and resid 447 through 454 removed outlier: 4.208A pdb=" N THR F 451 " --> pdb=" O GLU F 447 " (cutoff:3.500A) Processing helix chain 'F' and resid 489 through 503 removed outlier: 3.830A pdb=" N ILE F 493 " --> pdb=" O ASN F 489 " (cutoff:3.500A) Processing helix chain 'F' and resid 515 through 527 removed outlier: 3.617A pdb=" N ASN F 519 " --> pdb=" O TYR F 515 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N LYS F 524 " --> pdb=" O ALA F 520 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ILE F 525 " --> pdb=" O VAL F 521 " (cutoff:3.500A) Processing helix chain 'F' and resid 552 through 557 Processing helix chain 'F' and resid 561 through 566 removed outlier: 3.818A pdb=" N THR F 566 " --> pdb=" O ASN F 562 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 36 removed outlier: 3.802A pdb=" N SER E 36 " --> pdb=" O ASP E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 112 Processing helix chain 'E' and resid 116 through 125 removed outlier: 3.994A pdb=" N TYR E 120 " --> pdb=" O ASN E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 147 removed outlier: 3.502A pdb=" N LEU E 147 " --> pdb=" O GLU E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 181 removed outlier: 3.747A pdb=" N VAL E 181 " --> pdb=" O ARG E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 262 through 273 removed outlier: 4.312A pdb=" N VAL E 266 " --> pdb=" O PHE E 262 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ALA E 267 " --> pdb=" O SER E 263 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ASN E 268 " --> pdb=" O SER E 264 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS E 271 " --> pdb=" O ALA E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 299 removed outlier: 5.137A pdb=" N ILE E 293 " --> pdb=" O SER E 289 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU E 297 " --> pdb=" O ILE E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 320 Processing helix chain 'E' and resid 320 through 325 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 432 removed outlier: 3.678A pdb=" N ARG E 427 " --> pdb=" O ASN E 423 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LYS E 430 " --> pdb=" O CYS E 426 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR E 431 " --> pdb=" O ARG E 427 " (cutoff:3.500A) Processing helix chain 'E' and resid 446 through 456 removed outlier: 3.807A pdb=" N ASP E 450 " --> pdb=" O ALA E 446 " (cutoff:3.500A) Processing helix chain 'E' and resid 489 through 501 removed outlier: 4.807A pdb=" N VAL E 495 " --> pdb=" O PRO E 491 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ARG E 497 " --> pdb=" O ILE E 493 " (cutoff:3.500A) Processing helix chain 'E' and resid 503 through 507 removed outlier: 3.548A pdb=" N TRP E 506 " --> pdb=" O ASN E 503 " (cutoff:3.500A) Processing helix chain 'E' and resid 516 through 526 removed outlier: 4.402A pdb=" N LYS E 524 " --> pdb=" O ALA E 520 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE E 525 " --> pdb=" O VAL E 521 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 110 removed outlier: 3.720A pdb=" N ARG G 99 " --> pdb=" O ASN G 95 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 34 removed outlier: 3.601A pdb=" N ARG A 33 " --> pdb=" O PHE A 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 223 through 224 removed outlier: 5.756A pdb=" N ILE A 201 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N VAL A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N GLY A 203 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 327 through 328 removed outlier: 3.557A pdb=" N GLY A 327 " --> pdb=" O HIS A 347 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 338 through 341 removed outlier: 10.197A pdb=" N SER A 363 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N PHE A 334 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 389 through 390 removed outlier: 7.014A pdb=" N LEU A 389 " --> pdb=" O VAL B 131 " (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 543 through 544 Processing sheet with id=AA8, first strand: chain 'A' and resid 756 through 757 Processing sheet with id=AA9, first strand: chain 'A' and resid 821 through 822 Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 149 removed outlier: 3.659A pdb=" N TYR B 149 " --> pdb=" O ALA B 152 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA B 152 " --> pdb=" O TYR B 149 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU B 153 " --> pdb=" O ALA B 191 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 127 through 128 Processing sheet with id=AB3, first strand: chain 'D' and resid 142 through 143 removed outlier: 3.545A pdb=" N ASP D 143 " --> pdb=" O THR D 146 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 24 through 25 removed outlier: 3.722A pdb=" N LEU F 14 " --> pdb=" O LEU F 25 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 63 through 64 removed outlier: 3.590A pdb=" N TYR F 64 " --> pdb=" O TYR F 71 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 154 through 157 removed outlier: 3.704A pdb=" N GLU F 156 " --> pdb=" O HIS F 164 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 183 through 185 removed outlier: 3.609A pdb=" N TYR F 224 " --> pdb=" O TYR F 185 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 277 through 279 removed outlier: 6.603A pdb=" N SER F 278 " --> pdb=" O TYR F 398 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 330 through 332 removed outlier: 5.661A pdb=" N SER F 331 " --> pdb=" O PHE F 357 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'F' and resid 481 through 482 removed outlier: 3.537A pdb=" N THR F 481 " --> pdb=" O ILE F 488 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 511 through 512 removed outlier: 5.932A pdb=" N ILE F 512 " --> pdb=" O THR F 547 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL F 544 " --> pdb=" O LEU F 573 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ILE F 575 " --> pdb=" O VAL F 544 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N PHE F 546 " --> pdb=" O ILE F 575 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'E' and resid 14 through 15 removed outlier: 3.587A pdb=" N LEU E 14 " --> pdb=" O LEU E 25 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 69 through 71 removed outlier: 4.119A pdb=" N GLY E 66 " --> pdb=" O SER E 69 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 163 through 166 removed outlier: 7.191A pdb=" N HIS E 164 " --> pdb=" O ARG E 155 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL E 226 " --> pdb=" O THR E 183 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ARG E 186 " --> pdb=" O GLN E 194 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N GLN E 194 " --> pdb=" O ARG E 186 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 277 through 279 removed outlier: 5.567A pdb=" N VAL E 371 " --> pdb=" O VAL E 397 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N VAL E 305 " --> pdb=" O VAL E 372 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 530 through 532 removed outlier: 4.408A pdb=" N GLN E 531 " --> pdb=" O PHE E 511 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER E 513 " --> pdb=" O GLN E 531 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR E 547 " --> pdb=" O ILE E 512 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU E 573 " --> pdb=" O VAL E 544 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ILE E 575 " --> pdb=" O PHE E 546 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 30 through 35 removed outlier: 5.246A pdb=" N TYR G 31 " --> pdb=" O LEU G 42 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR G 79 " --> pdb=" O GLY G 82 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS G 86 " --> pdb=" O PHE G 75 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 53 through 57 671 hydrogen bonds defined for protein. 1893 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 30 hydrogen bonds 44 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 35 stacking parallelities Total time for adding SS restraints: 4.64 Time building geometry restraints manager: 2.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3631 1.31 - 1.44: 6360 1.44 - 1.57: 12114 1.57 - 1.70: 105 1.70 - 1.83: 224 Bond restraints: 22434 Sorted by residual: bond pdb=" CA ALA A 130 " pdb=" C ALA A 130 " ideal model delta sigma weight residual 1.523 1.383 0.140 1.34e-02 5.57e+03 1.09e+02 bond pdb=" CA MET A 899 " pdb=" C MET A 899 " ideal model delta sigma weight residual 1.522 1.407 0.116 1.37e-02 5.33e+03 7.14e+01 bond pdb=" CA GLN A 210 " pdb=" CB GLN A 210 " ideal model delta sigma weight residual 1.530 1.420 0.110 1.69e-02 3.50e+03 4.23e+01 bond pdb=" CA ALA A 176 " pdb=" C ALA A 176 " ideal model delta sigma weight residual 1.523 1.438 0.085 1.34e-02 5.57e+03 4.05e+01 bond pdb=" CA ASN B 100 " pdb=" C ASN B 100 " ideal model delta sigma weight residual 1.530 1.468 0.062 1.14e-02 7.69e+03 2.98e+01 ... (remaining 22429 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.77: 30226 3.77 - 7.53: 491 7.53 - 11.30: 34 11.30 - 15.06: 2 15.06 - 18.83: 1 Bond angle restraints: 30754 Sorted by residual: angle pdb=" N VAL C 22 " pdb=" CA VAL C 22 " pdb=" C VAL C 22 " ideal model delta sigma weight residual 112.83 105.42 7.41 9.90e-01 1.02e+00 5.60e+01 angle pdb=" CA CYS E 72 " pdb=" C CYS E 72 " pdb=" O CYS E 72 " ideal model delta sigma weight residual 117.94 121.40 -3.46 5.80e-01 2.97e+00 3.55e+01 angle pdb=" C ASP B 99 " pdb=" N ASN B 100 " pdb=" CA ASN B 100 " ideal model delta sigma weight residual 122.08 113.25 8.83 1.50e+00 4.44e-01 3.46e+01 angle pdb=" C PRO F 172 " pdb=" N ARG F 173 " pdb=" CA ARG F 173 " ideal model delta sigma weight residual 121.27 140.10 -18.83 3.40e+00 8.65e-02 3.07e+01 angle pdb=" N CYS F 358 " pdb=" CA CYS F 358 " pdb=" C CYS F 358 " ideal model delta sigma weight residual 107.73 114.78 -7.05 1.34e+00 5.57e-01 2.77e+01 ... (remaining 30749 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.88: 11976 25.88 - 51.76: 1178 51.76 - 77.64: 132 77.64 - 103.52: 14 103.52 - 129.40: 1 Dihedral angle restraints: 13301 sinusoidal: 5445 harmonic: 7856 Sorted by residual: dihedral pdb=" C4' G I 33 " pdb=" C3' G I 33 " pdb=" C2' G I 33 " pdb=" C1' G I 33 " ideal model delta sinusoidal sigma weight residual 36.34 -35.83 72.18 1 3.10e+00 1.04e-01 6.93e+02 dihedral pdb=" C4' G J 25 " pdb=" C3' G J 25 " pdb=" C2' G J 25 " pdb=" C1' G J 25 " ideal model delta sinusoidal sigma weight residual 36.35 -31.33 67.68 1 3.10e+00 1.04e-01 6.20e+02 dihedral pdb=" O4' G J 25 " pdb=" C4' G J 25 " pdb=" C3' G J 25 " pdb=" C2' G J 25 " ideal model delta sinusoidal sigma weight residual -35.15 26.92 -62.07 1 4.00e+00 6.25e-02 3.19e+02 ... (remaining 13298 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2510 0.063 - 0.127: 872 0.127 - 0.190: 122 0.190 - 0.253: 53 0.253 - 0.317: 8 Chirality restraints: 3565 Sorted by residual: chirality pdb=" C2' G J 25 " pdb=" C3' G J 25 " pdb=" O2' G J 25 " pdb=" C1' G J 25 " both_signs ideal model delta sigma weight residual False -2.79 -2.47 -0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" C2' G I 33 " pdb=" C3' G I 33 " pdb=" O2' G I 33 " pdb=" C1' G I 33 " both_signs ideal model delta sigma weight residual False -2.79 -2.49 -0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" P C J 30 " pdb=" OP1 C J 30 " pdb=" OP2 C J 30 " pdb=" O5' C J 30 " both_signs ideal model delta sigma weight residual True 2.17 -2.45 -0.28 2.00e-01 2.50e+01 1.92e+00 ... (remaining 3562 not shown) Planarity restraints: 3731 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP B 182 " 0.094 5.00e-02 4.00e+02 1.39e-01 3.09e+01 pdb=" N PRO B 183 " -0.240 5.00e-02 4.00e+02 pdb=" CA PRO B 183 " 0.075 5.00e-02 4.00e+02 pdb=" CD PRO B 183 " 0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 231 " -0.063 5.00e-02 4.00e+02 9.48e-02 1.44e+01 pdb=" N PRO A 232 " 0.164 5.00e-02 4.00e+02 pdb=" CA PRO A 232 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 232 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 132 " -0.062 5.00e-02 4.00e+02 9.26e-02 1.37e+01 pdb=" N PRO D 133 " 0.160 5.00e-02 4.00e+02 pdb=" CA PRO D 133 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO D 133 " -0.050 5.00e-02 4.00e+02 ... (remaining 3728 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 646 2.56 - 3.15: 21066 3.15 - 3.73: 35157 3.73 - 4.32: 48090 4.32 - 4.90: 76322 Nonbonded interactions: 181281 Sorted by model distance: nonbonded pdb=" O PHE E 145 " pdb=" OG SER E 148 " model vdw 1.979 3.040 nonbonded pdb=" O ARG A 533 " pdb=" ND2 ASN A 534 " model vdw 1.990 3.120 nonbonded pdb=" OH TYR F 269 " pdb=" O PHE F 291 " model vdw 1.996 3.040 nonbonded pdb=" O THR C 45 " pdb=" OG1 THR C 45 " model vdw 2.023 3.040 nonbonded pdb=" O SER E 264 " pdb=" ND2 ASN E 268 " model vdw 2.035 3.120 ... (remaining 181276 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 2 through 473 or resid 475 through 703)) selection = (chain 'F' and (resid 2 through 473 or resid 475 through 703)) } 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=0.41 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.150 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: 0.500 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 29.190 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 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 : 0.016 0.829 22467 Z= 0.881 Angle : 1.271 18.827 30782 Z= 0.693 Chirality : 0.065 0.317 3565 Planarity : 0.007 0.139 3731 Dihedral : 18.765 129.398 8233 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 38.61 Ramachandran Plot: Outliers : 1.52 % Allowed : 23.51 % Favored : 74.97 % Rotamer: Outliers : 14.07 % Allowed : 22.28 % Favored : 63.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -6.16 (0.11), residues: 2639 helix: -3.70 (0.10), residues: 940 sheet: -4.60 (0.26), residues: 214 loop : -4.47 (0.12), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 197 TYR 0.037 0.003 TYR E 269 PHE 0.031 0.003 PHE D 147 TRP 0.026 0.003 TRP A 916 HIS 0.016 0.002 HIS F 33 Details of bonding type rmsd/Z covalent geometry : bond 0.01511 / 0.68 (22434) covalent geometry : angle 1.24574 / 0.69 (30754) hydrogen bonds : bond 0.20648 / 13.09 ( 701) hydrogen bonds : angle 9.23951 / 6.33 ( 1937) metal coordination : bond 0.07432 / 3.60 ( 32) metal coordination : angle 8.41634 / 5.61 ( 28) Misc. bond : bond 0.82866 / 43.61 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 317 poor density : 118 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 TYR cc_start: 0.8690 (OUTLIER) cc_final: 0.8487 (t80) REVERT: A 110 MET cc_start: 0.7545 (mmp) cc_final: 0.7300 (mmm) REVERT: A 181 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.6753 (mtm180) REVERT: A 306 CYS cc_start: 0.7482 (OUTLIER) cc_final: 0.6937 (t) REVERT: A 366 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8961 (pp) REVERT: A 372 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.9124 (mp) REVERT: A 391 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8597 (mtpp) REVERT: A 445 ASP cc_start: 0.8548 (OUTLIER) cc_final: 0.8259 (p0) REVERT: A 511 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8720 (mtpp) REVERT: A 545 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8494 (mtmt) REVERT: A 553 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7856 (ptm-80) REVERT: A 610 GLU cc_start: 0.6641 (OUTLIER) cc_final: 0.6154 (mt-10) REVERT: A 636 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9123 (mp) REVERT: A 668 MET cc_start: 0.8595 (ttp) cc_final: 0.7997 (tmm) REVERT: A 750 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.7817 (mtm-85) REVERT: A 802 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7398 (mp0) REVERT: A 914 ARG cc_start: 0.8918 (OUTLIER) cc_final: 0.8475 (ptt-90) REVERT: B 65 GLN cc_start: 0.8772 (tm-30) cc_final: 0.8425 (tm-30) REVERT: B 82 LYS cc_start: 0.8720 (tppp) cc_final: 0.8386 (tppp) REVERT: C 38 ASP cc_start: 0.7549 (m-30) cc_final: 0.7290 (m-30) REVERT: D 12 TYR cc_start: 0.8718 (t80) cc_final: 0.8460 (t80) REVERT: D 67 MET cc_start: 0.7907 (ttp) cc_final: 0.7687 (tmm) REVERT: F 65 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.8979 (tt) REVERT: F 233 MET cc_start: 0.8099 (mmm) cc_final: 0.7710 (mmm) REVERT: F 325 LEU cc_start: 0.1647 (OUTLIER) cc_final: 0.0754 (tp) REVERT: F 421 TYR cc_start: 0.9161 (m-10) cc_final: 0.8906 (m-10) REVERT: F 440 THR cc_start: -0.0091 (OUTLIER) cc_final: -0.0588 (m) REVERT: E 405 LEU cc_start: 0.4870 (OUTLIER) cc_final: 0.4667 (tp) REVERT: E 541 TYR cc_start: 0.8565 (t80) cc_final: 0.8354 (t80) REVERT: G 12 MET cc_start: 0.7792 (tpp) cc_final: 0.7195 (tpp) REVERT: G 58 LYS cc_start: 0.8592 (tptp) cc_final: 0.8143 (tptp) REVERT: G 111 ARG cc_start: 0.8510 (mmm160) cc_final: 0.8282 (mmm160) outliers start: 317 outliers final: 224 residues processed: 421 average time/residue: 0.1257 time to fit residues: 86.5019 Evaluate side-chains 354 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 243 poor density : 111 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 TYR Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 93 CYS Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 163 TYR Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 181 ARG Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 306 CYS Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 391 LYS Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 421 ASP Chi-restraints excluded: chain A residue 433 SER Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 451 SER Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 468 GLN Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 483 TYR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 511 LYS Chi-restraints excluded: chain A residue 525 ASP Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 545 LYS Chi-restraints excluded: chain A residue 549 SER Chi-restraints excluded: chain A residue 553 ARG Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 564 SER Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 578 SER Chi-restraints excluded: chain A residue 606 TYR Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 611 ASN Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 658 GLU Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 704 VAL Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 724 GLN Chi-restraints excluded: chain A residue 734 ASN Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 748 TYR Chi-restraints excluded: chain A residue 750 ARG Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 773 GLN Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain A residue 791 ASN Chi-restraints excluded: chain A residue 799 CYS Chi-restraints excluded: chain A residue 802 GLU Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 825 ASP Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 845 ASP Chi-restraints excluded: chain A residue 858 ARG Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 892 HIS Chi-restraints excluded: chain A residue 894 GLU Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain A residue 913 SER Chi-restraints excluded: chain A residue 914 ARG Chi-restraints excluded: chain A residue 917 GLU Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 105 ASN Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain D residue 9 LEU Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 52 ASP Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 94 MET Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 120 ILE Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 140 ASN Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 11 GLN Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 31 TYR Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 224 TYR Chi-restraints excluded: chain F residue 230 HIS Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 288 LYS Chi-restraints excluded: chain F residue 317 LEU Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 385 SER Chi-restraints excluded: chain F residue 432 ILE Chi-restraints excluded: chain F residue 437 PHE Chi-restraints excluded: chain F residue 440 THR Chi-restraints excluded: chain F residue 455 LEU Chi-restraints excluded: chain F residue 530 THR Chi-restraints excluded: chain F residue 542 ASP Chi-restraints excluded: chain E residue 9 ASN Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 27 CYS Chi-restraints excluded: chain E residue 43 LEU Chi-restraints excluded: chain E residue 51 ASN Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 72 CYS Chi-restraints excluded: chain E residue 75 HIS Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 86 ASN Chi-restraints excluded: chain E residue 95 ASN Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain E residue 127 THR Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 164 HIS Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 301 SER Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 380 THR Chi-restraints excluded: chain E residue 383 ASP Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain E residue 388 ASN Chi-restraints excluded: chain E residue 405 LEU Chi-restraints excluded: chain E residue 455 LEU Chi-restraints excluded: chain E residue 482 HIS Chi-restraints excluded: chain E residue 492 GLN Chi-restraints excluded: chain E residue 532 THR Chi-restraints excluded: chain E residue 562 ASN Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 86 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 0.1980 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 40.0000 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 8.9990 chunk 111 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 209 ASN ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 354 GLN F 404 GLN ** F 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 519 ASN ** E 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.119764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.079584 restraints weight = 122305.869| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 6.05 r_work: 0.3124 rms_B_bonded: 5.47 restraints_weight: 2.0000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3116 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3116 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 22467 Z= 0.180 Angle : 0.864 14.547 30782 Z= 0.429 Chirality : 0.050 0.279 3565 Planarity : 0.006 0.101 3731 Dihedral : 12.971 117.700 3944 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 16.94 Ramachandran Plot: Outliers : 0.38 % Allowed : 12.19 % Favored : 87.43 % Rotamer: Outliers : 7.68 % Allowed : 24.83 % Favored : 67.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.48 (0.14), residues: 2639 helix: -2.01 (0.15), residues: 940 sheet: -4.04 (0.29), residues: 197 loop : -3.64 (0.13), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 427 TYR 0.033 0.002 TYR F 457 PHE 0.022 0.002 PHE F 357 TRP 0.017 0.002 TRP A 916 HIS 0.010 0.001 HIS F 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.18 (22434) covalent geometry : angle 0.84465 / 0.43 (30754) hydrogen bonds : bond 0.06908 / 4.47 ( 701) hydrogen bonds : angle 6.34247 / 4.36 ( 1937) metal coordination : bond 0.02013 / 1.27 ( 32) metal coordination : angle 6.10226 / 3.52 ( 28) Misc. bond : bond 0.00068 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 132 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 366 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8719 (pp) REVERT: A 553 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7772 (ptm-80) REVERT: A 626 MET cc_start: 0.8726 (OUTLIER) cc_final: 0.8473 (ttm) REVERT: A 735 ARG cc_start: 0.7000 (OUTLIER) cc_final: 0.6507 (mtm-85) REVERT: A 802 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.7685 (mp0) REVERT: B 56 GLN cc_start: 0.7854 (OUTLIER) cc_final: 0.7266 (pp30) REVERT: B 65 GLN cc_start: 0.8819 (tm-30) cc_final: 0.8573 (tm-30) REVERT: B 71 TYR cc_start: 0.8182 (t80) cc_final: 0.7962 (t80) REVERT: B 77 GLU cc_start: 0.8803 (tp30) cc_final: 0.8519 (tp30) REVERT: C 34 GLN cc_start: 0.8823 (tp40) cc_final: 0.8072 (tp-100) REVERT: C 38 ASP cc_start: 0.8243 (m-30) cc_final: 0.7665 (m-30) REVERT: C 52 MET cc_start: 0.8941 (tpp) cc_final: 0.8724 (tpt) REVERT: D 64 ASP cc_start: 0.8142 (OUTLIER) cc_final: 0.7761 (t70) REVERT: D 67 MET cc_start: 0.7614 (OUTLIER) cc_final: 0.7371 (tmm) REVERT: F 65 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8657 (tt) REVERT: F 233 MET cc_start: 0.8382 (mmm) cc_final: 0.8130 (mmm) REVERT: F 325 LEU cc_start: 0.3842 (OUTLIER) cc_final: 0.2706 (tp) REVERT: F 440 THR cc_start: 0.1075 (OUTLIER) cc_final: 0.0861 (t) REVERT: E 277 TYR cc_start: 0.6902 (OUTLIER) cc_final: 0.6355 (p90) REVERT: E 576 MET cc_start: 0.2324 (ptt) cc_final: 0.2051 (ptt) REVERT: G 10 ARG cc_start: 0.6413 (OUTLIER) cc_final: 0.4590 (mmp80) REVERT: G 58 LYS cc_start: 0.8967 (tptp) cc_final: 0.8688 (tptp) outliers start: 172 outliers final: 103 residues processed: 288 average time/residue: 0.1332 time to fit residues: 61.9512 Evaluate side-chains 234 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 118 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 525 ASP Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 553 ARG Chi-restraints excluded: chain A residue 626 MET Chi-restraints excluded: chain A residue 724 GLN Chi-restraints excluded: chain A residue 734 ASN Chi-restraints excluded: chain A residue 735 ARG Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 802 GLU Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 892 HIS Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 908 THR Chi-restraints excluded: chain A residue 913 SER Chi-restraints excluded: chain A residue 917 GLU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 142 CYS Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 67 MET Chi-restraints excluded: chain D residue 92 PHE Chi-restraints excluded: chain D residue 94 MET Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 165 LYS Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 11 GLN Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 224 TYR Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 288 LYS Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 437 PHE Chi-restraints excluded: chain F residue 440 THR Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 516 ASN Chi-restraints excluded: chain F residue 530 THR Chi-restraints excluded: chain F residue 532 THR Chi-restraints excluded: chain F residue 563 VAL Chi-restraints excluded: chain F residue 590 LEU Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 86 ASN Chi-restraints excluded: chain E residue 97 CYS Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 277 TYR Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 359 THR Chi-restraints excluded: chain E residue 424 SER Chi-restraints excluded: chain E residue 482 HIS Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 110 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 26 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 chunk 158 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 214 optimal weight: 0.0980 chunk 216 optimal weight: 0.7980 chunk 265 optimal weight: 2.9990 chunk 194 optimal weight: 0.1980 chunk 80 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 133 HIS ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 724 GLN B 176 ASN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 388 ASN ** E 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.132039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.090205 restraints weight = 124841.175| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 6.90 r_work: 0.3367 rms_B_bonded: 6.06 restraints_weight: 2.0000 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3365 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3365 r_free = 0.3365 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3365 r_free = 0.3365 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (13 function evaluations) r_final: 0.3365 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22467 Z= 0.138 Angle : 0.736 12.279 30782 Z= 0.364 Chirality : 0.046 0.269 3565 Planarity : 0.005 0.085 3731 Dihedral : 10.966 121.628 3659 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.79 % Favored : 88.99 % Rotamer: Outliers : 5.78 % Allowed : 25.98 % Favored : 68.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.49 (0.15), residues: 2639 helix: -0.90 (0.16), residues: 920 sheet: -3.88 (0.28), residues: 222 loop : -3.14 (0.14), residues: 1497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 74 TYR 0.028 0.002 TYR B 135 PHE 0.025 0.001 PHE F 357 TRP 0.020 0.002 TRP G 53 HIS 0.008 0.001 HIS E 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (22434) covalent geometry : angle 0.71961 / 0.36 (30754) hydrogen bonds : bond 0.05863 / 3.83 ( 701) hydrogen bonds : angle 5.51542 / 3.80 ( 1937) metal coordination : bond 0.01578 / 1.02 ( 32) metal coordination : angle 5.16313 / 3.08 ( 28) Misc. bond : bond 0.00040 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 141 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 478 LYS cc_start: 0.9090 (OUTLIER) cc_final: 0.8789 (ttmm) REVERT: A 657 ASN cc_start: 0.8616 (OUTLIER) cc_final: 0.8405 (t0) REVERT: A 668 MET cc_start: 0.8996 (ttp) cc_final: 0.8517 (tmm) REVERT: A 735 ARG cc_start: 0.7082 (OUTLIER) cc_final: 0.6468 (mtm-85) REVERT: A 802 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7812 (mp0) REVERT: A 917 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8391 (mt-10) REVERT: B 48 GLU cc_start: 0.8626 (tt0) cc_final: 0.8303 (tt0) REVERT: B 56 GLN cc_start: 0.7358 (OUTLIER) cc_final: 0.7035 (pp30) REVERT: B 65 GLN cc_start: 0.8771 (tm-30) cc_final: 0.8536 (tm-30) REVERT: B 71 TYR cc_start: 0.8194 (t80) cc_final: 0.7984 (t80) REVERT: B 77 GLU cc_start: 0.8873 (tp30) cc_final: 0.8637 (tp30) REVERT: C 21 ARG cc_start: 0.8926 (mmm160) cc_final: 0.8660 (mmm160) REVERT: C 34 GLN cc_start: 0.8909 (tp40) cc_final: 0.8140 (tp-100) REVERT: C 38 ASP cc_start: 0.8295 (m-30) cc_final: 0.7751 (m-30) REVERT: D 48 GLU cc_start: 0.8091 (pp20) cc_final: 0.7629 (pp20) REVERT: F 65 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8932 (tt) REVERT: F 233 MET cc_start: 0.8558 (mmm) cc_final: 0.8332 (mmm) REVERT: F 325 LEU cc_start: 0.4116 (OUTLIER) cc_final: 0.3071 (tp) REVERT: E 277 TYR cc_start: 0.6824 (OUTLIER) cc_final: 0.6334 (p90) REVERT: G 12 MET cc_start: 0.8395 (tpp) cc_final: 0.8106 (tpp) REVERT: G 58 LYS cc_start: 0.8947 (tptp) cc_final: 0.8626 (tptp) REVERT: G 111 ARG cc_start: 0.7727 (mmm160) cc_final: 0.7493 (mmm160) outliers start: 130 outliers final: 72 residues processed: 259 average time/residue: 0.1457 time to fit residues: 60.4427 Evaluate side-chains 207 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 126 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 482 CYS Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 525 ASP Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 734 ASN Chi-restraints excluded: chain A residue 735 ARG Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 802 GLU Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 892 HIS Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 913 SER Chi-restraints excluded: chain A residue 917 GLU Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 92 PHE Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 224 TYR Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 288 LYS Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 455 LEU Chi-restraints excluded: chain F residue 530 THR Chi-restraints excluded: chain F residue 563 VAL Chi-restraints excluded: chain F residue 572 ILE Chi-restraints excluded: chain E residue 86 ASN Chi-restraints excluded: chain E residue 185 TYR Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 277 TYR Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 388 ASN Chi-restraints excluded: chain E residue 424 SER Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 79 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 109 optimal weight: 4.9990 chunk 114 optimal weight: 0.7980 chunk 246 optimal weight: 10.0000 chunk 136 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 172 optimal weight: 10.0000 chunk 116 optimal weight: 10.0000 chunk 133 optimal weight: 9.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 507 ASN A 898 HIS ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 268 ASN ** F 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 519 ASN ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 388 ASN ** E 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.130684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.087989 restraints weight = 108768.399| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 6.33 r_work: 0.3351 rms_B_bonded: 5.05 restraints_weight: 2.0000 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3354 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3354 r_free = 0.3354 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3354 r_free = 0.3354 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3354 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 22467 Z= 0.175 Angle : 0.730 13.026 30782 Z= 0.359 Chirality : 0.045 0.271 3565 Planarity : 0.005 0.083 3731 Dihedral : 10.208 122.059 3607 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.22 % Favored : 89.56 % Rotamer: Outliers : 5.87 % Allowed : 25.94 % Favored : 68.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.20 (0.15), residues: 2639 helix: -0.67 (0.17), residues: 927 sheet: -3.57 (0.28), residues: 243 loop : -2.95 (0.14), residues: 1469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 427 TYR 0.025 0.002 TYR F 457 PHE 0.028 0.002 PHE F 357 TRP 0.020 0.001 TRP G 53 HIS 0.007 0.001 HIS A 898 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (22434) covalent geometry : angle 0.71513 / 0.36 (30754) hydrogen bonds : bond 0.05885 / 3.87 ( 701) hydrogen bonds : angle 5.41425 / 3.75 ( 1937) metal coordination : bond 0.02254 / 1.61 ( 32) metal coordination : angle 4.91461 / 2.88 ( 28) Misc. bond : bond 0.00078 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 127 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 478 LYS cc_start: 0.9093 (OUTLIER) cc_final: 0.8884 (ttmm) REVERT: A 735 ARG cc_start: 0.7060 (OUTLIER) cc_final: 0.6499 (mtm-85) REVERT: A 802 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7702 (mp0) REVERT: A 917 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8443 (mt-10) REVERT: B 48 GLU cc_start: 0.8699 (tt0) cc_final: 0.8349 (tt0) REVERT: B 56 GLN cc_start: 0.7321 (OUTLIER) cc_final: 0.7088 (pp30) REVERT: B 65 GLN cc_start: 0.8751 (tm-30) cc_final: 0.8471 (tm-30) REVERT: B 77 GLU cc_start: 0.8870 (tp30) cc_final: 0.8613 (tp30) REVERT: C 34 GLN cc_start: 0.8930 (tp40) cc_final: 0.8074 (tp-100) REVERT: C 38 ASP cc_start: 0.8292 (m-30) cc_final: 0.7686 (m-30) REVERT: F 65 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8770 (tt) REVERT: F 233 MET cc_start: 0.8591 (mmm) cc_final: 0.8364 (mmm) REVERT: F 325 LEU cc_start: 0.3838 (OUTLIER) cc_final: 0.2710 (tp) REVERT: E 260 ASP cc_start: 0.6644 (OUTLIER) cc_final: 0.5538 (m-30) REVERT: E 277 TYR cc_start: 0.6803 (OUTLIER) cc_final: 0.6288 (p90) REVERT: E 436 MET cc_start: 0.7657 (mmt) cc_final: 0.7452 (mmt) REVERT: G 53 TRP cc_start: 0.7256 (m100) cc_final: 0.7012 (m100) REVERT: G 58 LYS cc_start: 0.8845 (tptp) cc_final: 0.8481 (tptp) REVERT: G 87 TYR cc_start: 0.7741 (m-80) cc_final: 0.7508 (m-80) REVERT: G 111 ARG cc_start: 0.7733 (mmm160) cc_final: 0.7410 (mmm160) outliers start: 132 outliers final: 91 residues processed: 243 average time/residue: 0.1368 time to fit residues: 52.8056 Evaluate side-chains 220 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 120 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 525 ASP Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 734 ASN Chi-restraints excluded: chain A residue 735 ARG Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 802 GLU Chi-restraints excluded: chain A residue 845 ASP Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 892 HIS Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 913 SER Chi-restraints excluded: chain A residue 917 GLU Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 165 LYS Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 224 TYR Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 288 LYS Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 455 LEU Chi-restraints excluded: chain F residue 516 ASN Chi-restraints excluded: chain F residue 530 THR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 86 ASN Chi-restraints excluded: chain E residue 185 TYR Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 260 ASP Chi-restraints excluded: chain E residue 277 TYR Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 462 LYS Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 574 CYS Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 39 ARG Chi-restraints excluded: chain G residue 49 GLN Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 110 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 60 optimal weight: 0.6980 chunk 87 optimal weight: 0.6980 chunk 39 optimal weight: 7.9990 chunk 238 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 chunk 243 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 208 optimal weight: 3.9990 chunk 201 optimal weight: 5.9990 chunk 132 optimal weight: 0.8980 chunk 197 optimal weight: 10.0000 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 GLN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.130585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.088382 restraints weight = 102954.943| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 6.50 r_work: 0.3370 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3367 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3367 r_free = 0.3367 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3367 r_free = 0.3367 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3367 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 22467 Z= 0.162 Angle : 0.699 13.169 30782 Z= 0.344 Chirality : 0.044 0.272 3565 Planarity : 0.004 0.077 3731 Dihedral : 9.946 122.389 3603 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.06 % Favored : 89.71 % Rotamer: Outliers : 5.47 % Allowed : 26.51 % Favored : 68.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.97 (0.15), residues: 2639 helix: -0.51 (0.17), residues: 928 sheet: -3.40 (0.28), residues: 253 loop : -2.80 (0.14), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 74 TYR 0.024 0.002 TYR F 306 PHE 0.028 0.001 PHE F 357 TRP 0.011 0.001 TRP F 167 HIS 0.005 0.001 HIS F 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (22434) covalent geometry : angle 0.68490 / 0.34 (30754) hydrogen bonds : bond 0.05724 / 3.77 ( 701) hydrogen bonds : angle 5.24390 / 3.62 ( 1937) metal coordination : bond 0.02868 / 2.03 ( 32) metal coordination : angle 4.70604 / 2.72 ( 28) Misc. bond : bond 0.00058 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 131 time to evaluate : 0.769 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: A 478 LYS cc_start: 0.9081 (OUTLIER) cc_final: 0.8802 (ttmm) REVERT: A 735 ARG cc_start: 0.7113 (OUTLIER) cc_final: 0.6547 (mtm-85) REVERT: A 802 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7709 (mp0) REVERT: A 903 TYR cc_start: 0.7743 (t80) cc_final: 0.7383 (t80) REVERT: B 48 GLU cc_start: 0.8608 (tt0) cc_final: 0.8361 (tt0) REVERT: B 65 GLN cc_start: 0.8708 (tm-30) cc_final: 0.8460 (tm-30) REVERT: B 77 GLU cc_start: 0.8856 (tp30) cc_final: 0.8621 (tp30) REVERT: B 94 MET cc_start: 0.8587 (ttp) cc_final: 0.8354 (ttp) REVERT: C 34 GLN cc_start: 0.8890 (tp40) cc_final: 0.8034 (tp-100) REVERT: C 38 ASP cc_start: 0.8226 (m-30) cc_final: 0.7647 (m-30) REVERT: D 92 PHE cc_start: 0.8212 (OUTLIER) cc_final: 0.7313 (t80) REVERT: D 129 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7472 (mmm) REVERT: F 65 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.8961 (tt) REVERT: F 233 MET cc_start: 0.8717 (mmm) cc_final: 0.8446 (mmm) REVERT: F 325 LEU cc_start: 0.3017 (OUTLIER) cc_final: 0.1927 (tp) REVERT: F 437 PHE cc_start: 0.2931 (OUTLIER) cc_final: 0.0942 (m-10) REVERT: E 260 ASP cc_start: 0.6487 (OUTLIER) cc_final: 0.5224 (m-30) REVERT: E 277 TYR cc_start: 0.6612 (OUTLIER) cc_final: 0.5975 (p90) REVERT: E 436 MET cc_start: 0.7568 (mmt) cc_final: 0.7313 (mmt) REVERT: E 541 TYR cc_start: 0.8039 (t80) cc_final: 0.7609 (t80) REVERT: G 58 LYS cc_start: 0.8825 (tptp) cc_final: 0.8440 (tptp) REVERT: G 111 ARG cc_start: 0.7693 (mmm160) cc_final: 0.7305 (mmm160) outliers start: 123 outliers final: 83 residues processed: 241 average time/residue: 0.1249 time to fit residues: 48.0354 Evaluate side-chains 213 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 120 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 734 ASN Chi-restraints excluded: chain A residue 735 ARG Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 802 GLU Chi-restraints excluded: chain A residue 845 ASP Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 892 HIS Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 92 PHE Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 224 TYR Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 288 LYS Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 437 PHE Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 455 LEU Chi-restraints excluded: chain F residue 516 ASN Chi-restraints excluded: chain F residue 530 THR Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 185 TYR Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 260 ASP Chi-restraints excluded: chain E residue 277 TYR Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 424 SER Chi-restraints excluded: chain E residue 462 LYS Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 39 ARG Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 110 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 208 optimal weight: 9.9990 chunk 254 optimal weight: 1.9990 chunk 239 optimal weight: 6.9990 chunk 109 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 chunk 166 optimal weight: 10.0000 chunk 148 optimal weight: 9.9990 chunk 196 optimal weight: 20.0000 chunk 51 optimal weight: 2.9990 chunk 117 optimal weight: 6.9990 chunk 190 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.119600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.082407 restraints weight = 122768.668| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 5.70 r_work: 0.3116 rms_B_bonded: 5.31 restraints_weight: 2.0000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3081 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3081 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 22467 Z= 0.220 Angle : 0.736 14.346 30782 Z= 0.361 Chirality : 0.046 0.275 3565 Planarity : 0.005 0.074 3731 Dihedral : 9.737 123.278 3588 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.75 % Favored : 89.02 % Rotamer: Outliers : 5.96 % Allowed : 26.64 % Favored : 67.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.90 (0.15), residues: 2639 helix: -0.50 (0.17), residues: 926 sheet: -3.24 (0.29), residues: 237 loop : -2.75 (0.15), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 427 TYR 0.024 0.002 TYR F 306 PHE 0.028 0.002 PHE F 357 TRP 0.021 0.001 TRP G 53 HIS 0.005 0.001 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.22 (22434) covalent geometry : angle 0.72133 / 0.36 (30754) hydrogen bonds : bond 0.06039 / 3.97 ( 701) hydrogen bonds : angle 5.34091 / 3.70 ( 1937) metal coordination : bond 0.02338 / 1.63 ( 32) metal coordination : angle 4.90587 / 2.81 ( 28) Misc. bond : bond 0.00088 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 125 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 553 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.7716 (ptm-80) REVERT: A 735 ARG cc_start: 0.7147 (OUTLIER) cc_final: 0.6626 (mtm-85) REVERT: A 802 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.7744 (mp0) REVERT: A 906 MET cc_start: 0.7070 (mmm) cc_final: 0.6692 (mmm) REVERT: B 48 GLU cc_start: 0.8784 (tt0) cc_final: 0.8454 (tt0) REVERT: B 65 GLN cc_start: 0.8750 (tm-30) cc_final: 0.8483 (tm-30) REVERT: B 77 GLU cc_start: 0.8852 (tp30) cc_final: 0.8620 (tp30) REVERT: B 168 GLN cc_start: 0.8665 (mp10) cc_final: 0.8434 (mp10) REVERT: C 34 GLN cc_start: 0.8888 (tp40) cc_final: 0.7998 (tp-100) REVERT: C 38 ASP cc_start: 0.8330 (m-30) cc_final: 0.7691 (m-30) REVERT: D 129 MET cc_start: 0.8233 (OUTLIER) cc_final: 0.7513 (mmm) REVERT: F 65 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.8963 (tt) REVERT: F 233 MET cc_start: 0.8703 (mmm) cc_final: 0.8463 (mmm) REVERT: F 325 LEU cc_start: 0.3472 (OUTLIER) cc_final: 0.2297 (tp) REVERT: E 260 ASP cc_start: 0.6542 (OUTLIER) cc_final: 0.5349 (m-30) REVERT: E 277 TYR cc_start: 0.6566 (OUTLIER) cc_final: 0.6051 (p90) REVERT: E 436 MET cc_start: 0.7637 (mmt) cc_final: 0.7377 (mmt) REVERT: E 492 GLN cc_start: 0.1926 (OUTLIER) cc_final: 0.1655 (mp10) REVERT: E 541 TYR cc_start: 0.7974 (t80) cc_final: 0.7589 (t80) REVERT: G 58 LYS cc_start: 0.8886 (tptp) cc_final: 0.8557 (tptp) REVERT: G 111 ARG cc_start: 0.7620 (mmm160) cc_final: 0.7221 (mmm160) outliers start: 134 outliers final: 102 residues processed: 247 average time/residue: 0.1521 time to fit residues: 59.4376 Evaluate side-chains 230 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 119 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 553 ARG Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 734 ASN Chi-restraints excluded: chain A residue 735 ARG Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 802 GLU Chi-restraints excluded: chain A residue 845 ASP Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 892 HIS Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 92 PHE Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 165 LYS Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 224 TYR Chi-restraints excluded: chain F residue 230 HIS Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 288 LYS Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 340 VAL Chi-restraints excluded: chain F residue 455 LEU Chi-restraints excluded: chain F residue 516 ASN Chi-restraints excluded: chain F residue 530 THR Chi-restraints excluded: chain F residue 563 VAL Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 185 TYR Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 260 ASP Chi-restraints excluded: chain E residue 277 TYR Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 462 LYS Chi-restraints excluded: chain E residue 492 GLN Chi-restraints excluded: chain E residue 574 CYS Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 39 ARG Chi-restraints excluded: chain G residue 49 GLN Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 86 LYS Chi-restraints excluded: chain G residue 110 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 221 optimal weight: 8.9990 chunk 27 optimal weight: 0.9980 chunk 250 optimal weight: 4.9990 chunk 154 optimal weight: 20.0000 chunk 179 optimal weight: 40.0000 chunk 161 optimal weight: 7.9990 chunk 75 optimal weight: 0.7980 chunk 232 optimal weight: 20.0000 chunk 25 optimal weight: 3.9990 chunk 255 optimal weight: 4.9990 chunk 134 optimal weight: 0.0470 overall best weight: 2.1682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.130102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.086071 restraints weight = 133362.581| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 6.73 r_work: 0.3359 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3356 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3356 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 22467 Z= 0.190 Angle : 0.715 14.255 30782 Z= 0.351 Chirality : 0.045 0.276 3565 Planarity : 0.004 0.073 3731 Dihedral : 9.577 123.712 3585 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.06 % Favored : 89.75 % Rotamer: Outliers : 5.82 % Allowed : 27.30 % Favored : 66.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.76 (0.15), residues: 2639 helix: -0.38 (0.17), residues: 921 sheet: -3.01 (0.29), residues: 240 loop : -2.70 (0.15), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 96 TYR 0.047 0.002 TYR F 306 PHE 0.034 0.002 PHE F 357 TRP 0.022 0.001 TRP G 53 HIS 0.004 0.001 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.19 (22434) covalent geometry : angle 0.70091 / 0.35 (30754) hydrogen bonds : bond 0.05820 / 3.83 ( 701) hydrogen bonds : angle 5.22079 / 3.60 ( 1937) metal coordination : bond 0.02090 / 1.43 ( 32) metal coordination : angle 4.78636 / 2.76 ( 28) Misc. bond : bond 0.00065 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 121 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 607 SER cc_start: 0.9143 (OUTLIER) cc_final: 0.8881 (p) REVERT: A 657 ASN cc_start: 0.8731 (OUTLIER) cc_final: 0.8463 (t0) REVERT: A 735 ARG cc_start: 0.7145 (OUTLIER) cc_final: 0.6598 (mtm-85) REVERT: A 802 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7628 (mp0) REVERT: B 48 GLU cc_start: 0.8676 (tt0) cc_final: 0.8347 (tt0) REVERT: B 65 GLN cc_start: 0.8744 (tm-30) cc_final: 0.8458 (tm-30) REVERT: B 77 GLU cc_start: 0.8809 (tp30) cc_final: 0.8582 (tp30) REVERT: B 80 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.8449 (ttt180) REVERT: B 94 MET cc_start: 0.8655 (ttp) cc_final: 0.8444 (ttp) REVERT: C 34 GLN cc_start: 0.8949 (tp40) cc_final: 0.8067 (tp-100) REVERT: C 38 ASP cc_start: 0.8239 (m-30) cc_final: 0.7667 (m-30) REVERT: D 92 PHE cc_start: 0.8274 (OUTLIER) cc_final: 0.7361 (t80) REVERT: D 129 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.7545 (mmm) REVERT: F 65 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.9000 (tt) REVERT: F 233 MET cc_start: 0.8777 (mmm) cc_final: 0.8515 (mmm) REVERT: F 325 LEU cc_start: 0.2390 (OUTLIER) cc_final: 0.1294 (tp) REVERT: E 260 ASP cc_start: 0.6407 (OUTLIER) cc_final: 0.5126 (m-30) REVERT: E 436 MET cc_start: 0.7475 (mmt) cc_final: 0.7198 (mmt) REVERT: E 492 GLN cc_start: 0.1641 (OUTLIER) cc_final: 0.1395 (mp10) REVERT: E 541 TYR cc_start: 0.8039 (t80) cc_final: 0.7521 (t80) REVERT: G 58 LYS cc_start: 0.8761 (tptp) cc_final: 0.8338 (tptp) REVERT: G 111 ARG cc_start: 0.7650 (mmm160) cc_final: 0.7258 (mmm160) outliers start: 131 outliers final: 100 residues processed: 240 average time/residue: 0.1533 time to fit residues: 58.8074 Evaluate side-chains 229 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 118 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 734 ASN Chi-restraints excluded: chain A residue 735 ARG Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 802 GLU Chi-restraints excluded: chain A residue 845 ASP Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 892 HIS Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 80 ARG Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 92 PHE Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 165 LYS Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 224 TYR Chi-restraints excluded: chain F residue 230 HIS Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 288 LYS Chi-restraints excluded: chain F residue 325 LEU Chi-restraints excluded: chain F residue 340 VAL Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 455 LEU Chi-restraints excluded: chain F residue 516 ASN Chi-restraints excluded: chain F residue 530 THR Chi-restraints excluded: chain F residue 563 VAL Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 185 TYR Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 260 ASP Chi-restraints excluded: chain E residue 293 ILE Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 396 TYR Chi-restraints excluded: chain E residue 424 SER Chi-restraints excluded: chain E residue 462 LYS Chi-restraints excluded: chain E residue 492 GLN Chi-restraints excluded: chain E residue 574 CYS Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 39 ARG Chi-restraints excluded: chain G residue 49 GLN Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 110 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 65 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 188 optimal weight: 0.7980 chunk 142 optimal weight: 0.0980 chunk 19 optimal weight: 1.9990 chunk 178 optimal weight: 0.0570 chunk 208 optimal weight: 5.9990 chunk 158 optimal weight: 20.0000 chunk 213 optimal weight: 20.0000 chunk 34 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 395 HIS ** F 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.132918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.091890 restraints weight = 123199.611| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 7.17 r_work: 0.3349 rms_B_bonded: 6.05 restraints_weight: 2.0000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3355 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3355 r_free = 0.3355 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3355 r_free = 0.3355 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3355 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22467 Z= 0.121 Angle : 0.677 12.415 30782 Z= 0.330 Chirality : 0.043 0.270 3565 Planarity : 0.004 0.074 3731 Dihedral : 9.291 123.749 3583 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.23 % Favored : 90.58 % Rotamer: Outliers : 4.28 % Allowed : 28.98 % Favored : 66.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.53 (0.16), residues: 2639 helix: -0.12 (0.17), residues: 925 sheet: -3.08 (0.29), residues: 244 loop : -2.58 (0.15), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 96 TYR 0.046 0.001 TYR F 306 PHE 0.034 0.001 PHE F 357 TRP 0.019 0.001 TRP G 53 HIS 0.004 0.001 HIS E 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (22434) covalent geometry : angle 0.66457 / 0.33 (30754) hydrogen bonds : bond 0.05323 / 3.50 ( 701) hydrogen bonds : angle 4.88616 / 3.36 ( 1937) metal coordination : bond 0.01687 / 1.13 ( 32) metal coordination : angle 4.38697 / 2.59 ( 28) Misc. bond : bond 0.00013 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 136 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 MET cc_start: 0.8523 (mtm) cc_final: 0.8214 (mtm) REVERT: A 657 ASN cc_start: 0.8739 (OUTLIER) cc_final: 0.8449 (t0) REVERT: A 735 ARG cc_start: 0.7147 (OUTLIER) cc_final: 0.6548 (mtm-85) REVERT: A 802 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7747 (mp0) REVERT: B 48 GLU cc_start: 0.8748 (tt0) cc_final: 0.8494 (tt0) REVERT: B 65 GLN cc_start: 0.8771 (tm-30) cc_final: 0.8482 (tm-30) REVERT: B 77 GLU cc_start: 0.8835 (tp30) cc_final: 0.8630 (tp30) REVERT: B 80 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.8495 (ttt180) REVERT: B 94 MET cc_start: 0.8639 (ttp) cc_final: 0.8436 (ttp) REVERT: B 157 GLN cc_start: 0.8411 (pp30) cc_final: 0.8116 (pp30) REVERT: C 34 GLN cc_start: 0.8930 (tp40) cc_final: 0.8167 (tp-100) REVERT: C 38 ASP cc_start: 0.8402 (m-30) cc_final: 0.7831 (m-30) REVERT: D 129 MET cc_start: 0.8272 (OUTLIER) cc_final: 0.7578 (mmm) REVERT: F 65 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8760 (tt) REVERT: F 233 MET cc_start: 0.8856 (mmm) cc_final: 0.8632 (mmm) REVERT: F 437 PHE cc_start: 0.2952 (OUTLIER) cc_final: 0.1456 (m-10) REVERT: E 260 ASP cc_start: 0.6756 (OUTLIER) cc_final: 0.5756 (m-30) REVERT: E 436 MET cc_start: 0.7610 (mmt) cc_final: 0.7343 (mmt) REVERT: E 462 LYS cc_start: 0.3603 (OUTLIER) cc_final: 0.3223 (mtmm) REVERT: E 492 GLN cc_start: 0.2196 (OUTLIER) cc_final: 0.1902 (mp10) REVERT: E 541 TYR cc_start: 0.7938 (t80) cc_final: 0.7631 (t80) REVERT: G 39 ARG cc_start: 0.7329 (OUTLIER) cc_final: 0.7093 (ttt90) REVERT: G 58 LYS cc_start: 0.8862 (tptp) cc_final: 0.8547 (tptp) REVERT: G 87 TYR cc_start: 0.7835 (m-80) cc_final: 0.7289 (m-80) REVERT: G 89 TYR cc_start: 0.5728 (m-10) cc_final: 0.4893 (m-80) REVERT: G 111 ARG cc_start: 0.7801 (mmm160) cc_final: 0.7372 (mmm160) outliers start: 96 outliers final: 67 residues processed: 224 average time/residue: 0.1584 time to fit residues: 55.9436 Evaluate side-chains 201 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 123 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 734 ASN Chi-restraints excluded: chain A residue 735 ARG Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 802 GLU Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 892 HIS Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 80 ARG Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 165 LYS Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 224 TYR Chi-restraints excluded: chain F residue 230 HIS Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 288 LYS Chi-restraints excluded: chain F residue 340 VAL Chi-restraints excluded: chain F residue 437 PHE Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 516 ASN Chi-restraints excluded: chain F residue 530 THR Chi-restraints excluded: chain E residue 185 TYR Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 260 ASP Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 462 LYS Chi-restraints excluded: chain E residue 492 GLN Chi-restraints excluded: chain E residue 515 TYR Chi-restraints excluded: chain E residue 574 CYS Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 39 ARG Chi-restraints excluded: chain G residue 49 GLN Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 86 LYS Chi-restraints excluded: chain G residue 110 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 155 optimal weight: 0.7980 chunk 126 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 142 optimal weight: 0.0000 chunk 3 optimal weight: 3.9990 chunk 258 optimal weight: 9.9990 chunk 100 optimal weight: 7.9990 chunk 163 optimal weight: 7.9990 chunk 170 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 overall best weight: 2.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 ASN D 105 ASN D 109 ASN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 95 ASN ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 470 GLN ** E 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.129892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.088107 restraints weight = 134606.840| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 6.45 r_work: 0.3321 rms_B_bonded: 5.24 restraints_weight: 2.0000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3324 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3324 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.140 22467 Z= 0.214 Angle : 0.734 13.954 30782 Z= 0.357 Chirality : 0.045 0.273 3565 Planarity : 0.004 0.069 3731 Dihedral : 9.191 124.609 3573 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.99 % Favored : 89.86 % Rotamer: Outliers : 4.06 % Allowed : 29.55 % Favored : 66.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.62 (0.16), residues: 2639 helix: -0.26 (0.17), residues: 931 sheet: -3.08 (0.29), residues: 251 loop : -2.59 (0.15), residues: 1457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 96 TYR 0.036 0.002 TYR F 306 PHE 0.029 0.002 PHE F 357 TRP 0.021 0.001 TRP G 53 HIS 0.005 0.001 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.21 (22434) covalent geometry : angle 0.71800 / 0.36 (30754) hydrogen bonds : bond 0.05813 / 3.81 ( 701) hydrogen bonds : angle 5.08782 / 3.49 ( 1937) metal coordination : bond 0.02953 / 2.18 ( 32) metal coordination : angle 5.13845 / 3.38 ( 28) Misc. bond : bond 0.00080 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 128 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 607 SER cc_start: 0.9207 (OUTLIER) cc_final: 0.8921 (p) REVERT: A 657 ASN cc_start: 0.8771 (OUTLIER) cc_final: 0.8529 (t0) REVERT: A 735 ARG cc_start: 0.7141 (OUTLIER) cc_final: 0.6589 (mtm-85) REVERT: A 802 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7681 (mp0) REVERT: B 48 GLU cc_start: 0.8681 (tt0) cc_final: 0.8444 (tt0) REVERT: B 65 GLN cc_start: 0.8769 (tm-30) cc_final: 0.8481 (tm-30) REVERT: B 77 GLU cc_start: 0.8796 (tp30) cc_final: 0.8575 (tp30) REVERT: B 80 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.8409 (ttt180) REVERT: B 157 GLN cc_start: 0.8394 (pp30) cc_final: 0.8086 (pp30) REVERT: C 34 GLN cc_start: 0.8926 (tp40) cc_final: 0.8023 (tp-100) REVERT: C 38 ASP cc_start: 0.8327 (m-30) cc_final: 0.7760 (m-30) REVERT: D 129 MET cc_start: 0.8254 (OUTLIER) cc_final: 0.7477 (mmm) REVERT: F 65 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.8947 (tt) REVERT: F 233 MET cc_start: 0.8853 (mmm) cc_final: 0.8615 (mmm) REVERT: E 260 ASP cc_start: 0.6758 (OUTLIER) cc_final: 0.5696 (m-30) REVERT: E 436 MET cc_start: 0.7558 (mmt) cc_final: 0.7271 (mmt) REVERT: E 462 LYS cc_start: 0.3550 (OUTLIER) cc_final: 0.3120 (mtmm) REVERT: E 492 GLN cc_start: 0.1931 (OUTLIER) cc_final: 0.1646 (mp10) REVERT: E 541 TYR cc_start: 0.8004 (t80) cc_final: 0.7632 (t80) REVERT: G 58 LYS cc_start: 0.8781 (tptp) cc_final: 0.8464 (tptp) REVERT: G 111 ARG cc_start: 0.7718 (mmm160) cc_final: 0.7313 (mmm160) outliers start: 91 outliers final: 75 residues processed: 213 average time/residue: 0.1583 time to fit residues: 53.2294 Evaluate side-chains 207 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 122 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 734 ASN Chi-restraints excluded: chain A residue 735 ARG Chi-restraints excluded: chain A residue 755 MET Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 802 GLU Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 892 HIS Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 80 ARG Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 165 LYS Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 182 TRP Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 224 TYR Chi-restraints excluded: chain F residue 230 HIS Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 258 ILE Chi-restraints excluded: chain F residue 288 LYS Chi-restraints excluded: chain F residue 340 VAL Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 516 ASN Chi-restraints excluded: chain F residue 530 THR Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 260 ASP Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 462 LYS Chi-restraints excluded: chain E residue 492 GLN Chi-restraints excluded: chain E residue 515 TYR Chi-restraints excluded: chain E residue 574 CYS Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 49 GLN Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 86 LYS Chi-restraints excluded: chain G residue 110 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 241 optimal weight: 0.9990 chunk 216 optimal weight: 20.0000 chunk 43 optimal weight: 0.8980 chunk 215 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 101 optimal weight: 0.9980 chunk 140 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 219 optimal weight: 5.9990 chunk 98 optimal weight: 0.8980 chunk 221 optimal weight: 9.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 95 ASN ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 349 ASN ** E 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 464 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.132550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.089513 restraints weight = 112715.074| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 6.24 r_work: 0.3417 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3413 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3413 r_free = 0.3413 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3413 r_free = 0.3413 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3413 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 22467 Z= 0.124 Angle : 0.683 12.491 30782 Z= 0.332 Chirality : 0.043 0.271 3565 Planarity : 0.004 0.072 3731 Dihedral : 9.070 124.619 3573 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.51 % Favored : 91.34 % Rotamer: Outliers : 3.48 % Allowed : 30.13 % Favored : 66.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.36 (0.16), residues: 2639 helix: -0.01 (0.17), residues: 923 sheet: -2.64 (0.32), residues: 227 loop : -2.52 (0.15), residues: 1489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 51 TYR 0.033 0.001 TYR F 306 PHE 0.027 0.001 PHE F 357 TRP 0.019 0.001 TRP G 53 HIS 0.004 0.001 HIS E 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (22434) covalent geometry : angle 0.66950 / 0.33 (30754) hydrogen bonds : bond 0.05307 / 3.48 ( 701) hydrogen bonds : angle 4.81995 / 3.28 ( 1937) metal coordination : bond 0.02068 / 1.46 ( 32) metal coordination : angle 4.54416 / 2.85 ( 28) Misc. bond : bond 0.00004 / 0.00 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5278 Ramachandran restraints generated. 2639 Oldfield, 0 Emsley, 2639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 128 time to evaluate : 0.873 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: A 657 ASN cc_start: 0.8696 (OUTLIER) cc_final: 0.8475 (t0) REVERT: A 735 ARG cc_start: 0.7092 (OUTLIER) cc_final: 0.6507 (mtm-85) REVERT: A 802 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7697 (mp0) REVERT: B 65 GLN cc_start: 0.8605 (tm-30) cc_final: 0.8392 (tm-30) REVERT: B 80 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.8417 (ttt180) REVERT: B 157 GLN cc_start: 0.8329 (pp30) cc_final: 0.8020 (pp30) REVERT: C 34 GLN cc_start: 0.8816 (tp40) cc_final: 0.8037 (tp-100) REVERT: C 38 ASP cc_start: 0.8276 (m-30) cc_final: 0.7710 (m-30) REVERT: D 129 MET cc_start: 0.8190 (OUTLIER) cc_final: 0.7419 (mmm) REVERT: F 65 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8906 (tt) REVERT: F 233 MET cc_start: 0.8861 (mmm) cc_final: 0.8578 (mmm) REVERT: E 260 ASP cc_start: 0.6603 (OUTLIER) cc_final: 0.5453 (m-30) REVERT: E 429 MET cc_start: 0.8157 (mtm) cc_final: 0.7832 (mtm) REVERT: E 436 MET cc_start: 0.7386 (mmt) cc_final: 0.7087 (mmt) REVERT: E 462 LYS cc_start: 0.3318 (OUTLIER) cc_final: 0.2811 (mtmm) REVERT: E 492 GLN cc_start: 0.1519 (OUTLIER) cc_final: 0.1280 (mp10) REVERT: E 541 TYR cc_start: 0.7996 (t80) cc_final: 0.7514 (t80) REVERT: G 58 LYS cc_start: 0.8786 (tptp) cc_final: 0.8412 (tptp) REVERT: G 87 TYR cc_start: 0.7743 (m-80) cc_final: 0.7164 (m-80) REVERT: G 89 TYR cc_start: 0.5623 (m-10) cc_final: 0.4807 (m-80) REVERT: G 111 ARG cc_start: 0.7667 (mmm160) cc_final: 0.7339 (mmm160) outliers start: 78 outliers final: 63 residues processed: 202 average time/residue: 0.1569 time to fit residues: 50.3500 Evaluate side-chains 193 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 121 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 295 HIS Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 544 LEU Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 657 ASN Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 734 ASN Chi-restraints excluded: chain A residue 735 ARG Chi-restraints excluded: chain A residue 755 MET Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 802 GLU Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 892 HIS Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 80 ARG Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 224 TYR Chi-restraints excluded: chain F residue 230 HIS Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 288 LYS Chi-restraints excluded: chain F residue 340 VAL Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 455 LEU Chi-restraints excluded: chain F residue 516 ASN Chi-restraints excluded: chain F residue 530 THR Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 260 ASP Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 462 LYS Chi-restraints excluded: chain E residue 492 GLN Chi-restraints excluded: chain E residue 515 TYR Chi-restraints excluded: chain E residue 574 CYS Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 49 GLN Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 86 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 257 optimal weight: 20.0000 chunk 11 optimal weight: 0.9990 chunk 245 optimal weight: 6.9990 chunk 197 optimal weight: 9.9990 chunk 230 optimal weight: 7.9990 chunk 175 optimal weight: 6.9990 chunk 190 optimal weight: 7.9990 chunk 178 optimal weight: 0.0070 chunk 203 optimal weight: 0.0770 chunk 67 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 overall best weight: 1.6162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 548 GLN ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 268 ASN ** E 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.131437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.088011 restraints weight = 141779.059| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 6.96 r_work: 0.3346 rms_B_bonded: 5.38 restraints_weight: 2.0000 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3348 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3348 r_free = 0.3348 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3348 r_free = 0.3348 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3348 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 22467 Z= 0.158 Angle : 0.706 16.840 30782 Z= 0.340 Chirality : 0.044 0.272 3565 Planarity : 0.004 0.069 3731 Dihedral : 8.875 125.325 3562 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.19 % Favored : 90.66 % Rotamer: Outliers : 3.75 % Allowed : 29.69 % Favored : 66.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.36 (0.16), residues: 2639 helix: -0.06 (0.17), residues: 926 sheet: -2.58 (0.31), residues: 241 loop : -2.49 (0.15), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 51 TYR 0.030 0.001 TYR F 306 PHE 0.023 0.001 PHE F 357 TRP 0.015 0.001 TRP G 53 HIS 0.003 0.001 HIS E 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (22434) covalent geometry : angle 0.69193 / 0.34 (30754) hydrogen bonds : bond 0.05505 / 3.61 ( 701) hydrogen bonds : angle 4.85811 / 3.31 ( 1937) metal coordination : bond 0.01974 / 1.38 ( 32) metal coordination : angle 4.72777 / 2.97 ( 28) Misc. bond : bond 0.00057 / 0.03 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8059.25 seconds wall clock time: 138 minutes 20.69 seconds (8300.69 seconds total)