Starting phenix.real_space_refine on Thu May 22 00:54:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gwn_34317/05_2025/8gwn_34317.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gwn_34317/05_2025/8gwn_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8gwn_34317/05_2025/8gwn_34317.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gwn_34317/05_2025/8gwn_34317.map" model { file = "/net/cci-nas-00/data/ceres_data/8gwn_34317/05_2025/8gwn_34317.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gwn_34317/05_2025/8gwn_34317.cif" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2} 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, 'ASN:plan1': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "I" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 545 Classifications: {'RNA': 25} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 16, 'rna3p_pyr': 8} Link IDs: {'rna3p': 24} Chain: "J" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 565 Classifications: {'RNA': 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: {'ARG:plan': 5, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP: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: {'ARG:plan': 5, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP: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: {'ARG:plan': 5, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP: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: {'ARG:plan': 5, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP: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: 18.93, per 1000 atoms: 0.87 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: 6.43 Conformation dependent library (CDL) restraints added in 3.9 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: 8.27 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: 7.75 Time building geometry restraints manager: 7.42 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: 30255 3.77 - 7.53: 462 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: 12115 25.88 - 51.76: 1192 51.76 - 77.64: 203 77.64 - 103.52: 14 103.52 - 129.40: 1 Dihedral angle restraints: 13525 sinusoidal: 5669 harmonic: 7856 Sorted by residual: dihedral pdb=" CA TRP B 182 " pdb=" C TRP B 182 " pdb=" N PRO B 183 " pdb=" CA PRO B 183 " ideal model delta harmonic sigma weight residual 180.00 133.36 46.64 0 5.00e+00 4.00e-02 8.70e+01 dihedral pdb=" CA TYR A 903 " pdb=" C TYR A 903 " pdb=" N SER A 904 " pdb=" CA SER A 904 " ideal model delta harmonic sigma weight residual 180.00 143.29 36.71 0 5.00e+00 4.00e-02 5.39e+01 dihedral pdb=" CA VAL A 848 " pdb=" C VAL A 848 " pdb=" N LYS A 849 " pdb=" CA LYS A 849 " ideal model delta harmonic sigma weight residual 180.00 144.69 35.31 0 5.00e+00 4.00e-02 4.99e+01 ... (remaining 13522 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2359 0.055 - 0.109: 974 0.109 - 0.164: 199 0.164 - 0.218: 30 0.218 - 0.273: 3 Chirality restraints: 3565 Sorted by residual: chirality pdb=" CA MET A 899 " pdb=" N MET A 899 " pdb=" C MET A 899 " pdb=" CB MET A 899 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA ALA A 130 " pdb=" N ALA A 130 " pdb=" C ALA A 130 " pdb=" CB ALA A 130 " both_signs ideal model delta sigma weight residual False 2.48 2.22 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA ARG G 10 " pdb=" N ARG G 10 " pdb=" C ARG G 10 " pdb=" CB ARG G 10 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.35e+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 593 or resid 701 throug \ h 703)) selection = (chain 'F' and (resid 2 through 473 or resid 475 through 593 or resid 701 throug \ h 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: 7.510 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: 0.020 Extract box with map and model: 0.890 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 68.780 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 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= 0.882 Angle : 1.255 18.827 30782 Z= 0.694 Chirality : 0.059 0.273 3565 Planarity : 0.007 0.139 3731 Dihedral : 19.479 129.398 8457 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.026 0.003 TRP A 916 HIS 0.016 0.002 HIS F 33 PHE 0.031 0.003 PHE D 147 TYR 0.037 0.003 TYR E 269 ARG 0.014 0.001 ARG A 197 Details of bonding type rmsd hydrogen bonds : bond 0.20648 ( 701) hydrogen bonds : angle 9.23951 ( 1937) metal coordination : bond 0.07432 ( 32) metal coordination : angle 8.41634 ( 28) covalent geometry : bond 0.01509 (22434) covalent geometry : angle 1.22991 (30754) Misc. bond : bond 0.82866 ( 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 : 2.421 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: 0.2974 time to fit residues: 198.6554 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 : 2.403 ------------------------------------------------------------------------------- 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 224 optimal weight: 9.9990 chunk 201 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 135 optimal weight: 9.9990 chunk 107 optimal weight: 0.9990 chunk 208 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 155 optimal weight: 40.0000 chunk 241 optimal weight: 0.7980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.120174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.080656 restraints weight = 94327.140| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 5.42 r_work: 0.3161 rms_B_bonded: 5.05 restraints_weight: 2.0000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3158 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3159 r_free = 0.3159 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3159 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 22467 Z= 0.172 Angle : 0.833 14.180 30782 Z= 0.423 Chirality : 0.046 0.214 3565 Planarity : 0.006 0.102 3731 Dihedral : 15.517 120.855 4168 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.38 % Allowed : 11.32 % Favored : 88.30 % Rotamer: Outliers : 7.59 % Allowed : 24.53 % Favored : 67.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.42 (0.14), residues: 2639 helix: -1.94 (0.15), residues: 937 sheet: -4.03 (0.29), residues: 197 loop : -3.61 (0.13), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 916 HIS 0.010 0.001 HIS F 33 PHE 0.022 0.002 PHE F 357 TYR 0.034 0.002 TYR F 457 ARG 0.008 0.001 ARG E 427 Details of bonding type rmsd hydrogen bonds : bond 0.06844 ( 701) hydrogen bonds : angle 6.26470 ( 1937) metal coordination : bond 0.01914 ( 32) metal coordination : angle 6.09984 ( 28) covalent geometry : bond 0.00371 (22434) covalent geometry : angle 0.81238 (30754) Misc. bond : bond 0.00193 ( 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 303 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 133 time to evaluate : 2.322 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: 0.8925 (OUTLIER) cc_final: 0.8724 (pp) REVERT: A 553 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7767 (ptm-80) REVERT: A 626 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.8462 (ttm) REVERT: A 802 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.7604 (mp0) REVERT: B 55 MET cc_start: 0.8387 (tpt) cc_final: 0.8163 (tpt) REVERT: B 56 GLN cc_start: 0.7758 (OUTLIER) cc_final: 0.7215 (pp30) REVERT: B 65 GLN cc_start: 0.8775 (tm-30) cc_final: 0.8560 (tm-30) REVERT: B 71 TYR cc_start: 0.8100 (t80) cc_final: 0.7877 (t80) REVERT: B 77 GLU cc_start: 0.8781 (tp30) cc_final: 0.8502 (tp30) REVERT: C 34 GLN cc_start: 0.8811 (tp40) cc_final: 0.8073 (tp-100) REVERT: C 38 ASP cc_start: 0.8211 (m-30) cc_final: 0.7619 (m-30) REVERT: C 52 MET cc_start: 0.8895 (tpp) cc_final: 0.8683 (tpt) REVERT: D 67 MET cc_start: 0.7537 (OUTLIER) cc_final: 0.7305 (tmm) REVERT: D 185 ILE cc_start: 0.9030 (mp) cc_final: 0.8819 (mm) REVERT: F 65 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8511 (tt) REVERT: F 233 MET cc_start: 0.8447 (mmm) cc_final: 0.8197 (mmm) REVERT: F 325 LEU cc_start: 0.3822 (OUTLIER) cc_final: 0.2673 (tp) REVERT: F 440 THR cc_start: 0.1003 (OUTLIER) cc_final: 0.0791 (t) REVERT: E 277 TYR cc_start: 0.6894 (OUTLIER) cc_final: 0.6336 (p90) REVERT: E 576 MET cc_start: 0.2237 (ptt) cc_final: 0.1975 (ptt) REVERT: G 10 ARG cc_start: 0.6390 (OUTLIER) cc_final: 0.4723 (mmp80) REVERT: G 58 LYS cc_start: 0.8924 (tptp) cc_final: 0.8605 (tptp) outliers start: 170 outliers final: 99 residues processed: 287 average time/residue: 0.3151 time to fit residues: 142.5180 Evaluate side-chains 226 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 116 time to evaluate : 2.497 ------------------------------------------------------------------------------- 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 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 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 704 VAL 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 11 SER 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 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 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 35 LEU 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 158 GLN 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 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 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 68 optimal weight: 6.9990 chunk 208 optimal weight: 20.0000 chunk 48 optimal weight: 7.9990 chunk 144 optimal weight: 9.9990 chunk 147 optimal weight: 5.9990 chunk 127 optimal weight: 0.9990 chunk 137 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 167 optimal weight: 20.0000 chunk 86 optimal weight: 0.8980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 507 ASN A 724 GLN B 176 ASN ** 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 354 GLN ** 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** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.118591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.078992 restraints weight = 118777.280| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 5.46 r_work: 0.3090 rms_B_bonded: 5.22 restraints_weight: 2.0000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3084 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3084 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 22467 Z= 0.218 Angle : 0.770 14.876 30782 Z= 0.388 Chirality : 0.045 0.236 3565 Planarity : 0.005 0.084 3731 Dihedral : 14.454 125.087 3880 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.27 % Allowed : 12.53 % Favored : 87.20 % Rotamer: Outliers : 7.01 % Allowed : 26.03 % Favored : 66.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.77 (0.14), residues: 2639 helix: -1.23 (0.16), residues: 919 sheet: -3.75 (0.29), residues: 227 loop : -3.28 (0.14), residues: 1493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP G 53 HIS 0.009 0.001 HIS F 33 PHE 0.028 0.002 PHE F 357 TYR 0.028 0.002 TYR F 217 ARG 0.007 0.001 ARG G 74 Details of bonding type rmsd hydrogen bonds : bond 0.06569 ( 701) hydrogen bonds : angle 5.89936 ( 1937) metal coordination : bond 0.01913 ( 32) metal coordination : angle 5.88389 ( 28) covalent geometry : bond 0.00496 (22434) covalent geometry : angle 0.74925 (30754) Misc. bond : bond 0.00117 ( 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 288 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 131 time to evaluate : 2.377 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 366 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8805 (pp) REVERT: A 478 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8860 (ttmm) REVERT: A 553 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.7781 (ptm-80) REVERT: A 607 SER cc_start: 0.9277 (OUTLIER) cc_final: 0.9003 (p) REVERT: A 657 ASN cc_start: 0.8630 (OUTLIER) cc_final: 0.8352 (t0) REVERT: A 735 ARG cc_start: 0.7080 (OUTLIER) cc_final: 0.6568 (mtm-85) REVERT: A 802 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.7768 (mp0) REVERT: A 917 GLU cc_start: 0.8974 (OUTLIER) cc_final: 0.8752 (mt-10) REVERT: B 48 GLU cc_start: 0.8687 (tt0) cc_final: 0.8367 (tt0) REVERT: B 56 GLN cc_start: 0.7572 (OUTLIER) cc_final: 0.7337 (pp30) REVERT: B 65 GLN cc_start: 0.8792 (tm-30) cc_final: 0.8534 (tm-30) REVERT: B 71 TYR cc_start: 0.8191 (t80) cc_final: 0.7951 (t80) REVERT: B 77 GLU cc_start: 0.8833 (tp30) cc_final: 0.8538 (tp30) REVERT: C 21 ARG cc_start: 0.8915 (mmm160) cc_final: 0.8584 (mmm160) REVERT: C 34 GLN cc_start: 0.8870 (tp40) cc_final: 0.7987 (tp-100) REVERT: C 38 ASP cc_start: 0.8274 (m-30) cc_final: 0.7654 (m-30) REVERT: C 52 MET cc_start: 0.8975 (tpp) cc_final: 0.8723 (tpt) REVERT: F 65 LEU cc_start: 0.9428 (OUTLIER) cc_final: 0.9026 (tt) REVERT: F 233 MET cc_start: 0.8493 (mmm) cc_final: 0.8266 (mmm) REVERT: F 325 LEU cc_start: 0.3311 (OUTLIER) cc_final: 0.2180 (tp) REVERT: E 277 TYR cc_start: 0.6841 (OUTLIER) cc_final: 0.6278 (p90) REVERT: G 12 MET cc_start: 0.8255 (tpp) cc_final: 0.7985 (tpp) REVERT: G 58 LYS cc_start: 0.8935 (tptp) cc_final: 0.8577 (tptp) REVERT: G 111 ARG cc_start: 0.7415 (mmm160) cc_final: 0.7167 (mmm160) outliers start: 157 outliers final: 102 residues processed: 270 average time/residue: 0.3079 time to fit residues: 131.5812 Evaluate side-chains 237 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 123 time to evaluate : 2.634 ------------------------------------------------------------------------------- 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 114 ILE 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 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 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 435 VAL 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 544 LEU Chi-restraints excluded: chain A residue 553 ARG Chi-restraints excluded: chain A residue 607 SER 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 758 LEU Chi-restraints excluded: chain A residue 772 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 883 LEU 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 34 VAL 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 85 SER 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 119 ILE Chi-restraints excluded: chain B residue 132 ILE Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain C residue 66 VAL 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 78 ASP Chi-restraints excluded: chain D residue 83 VAL 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 112 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 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 280 LEU Chi-restraints excluded: chain F residue 288 LYS Chi-restraints excluded: chain F residue 325 LEU 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 572 ILE 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 388 ASN Chi-restraints excluded: chain E residue 455 LEU 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 77 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 155 optimal weight: 30.0000 chunk 238 optimal weight: 10.0000 chunk 236 optimal weight: 3.9990 chunk 217 optimal weight: 2.9990 chunk 225 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 161 optimal weight: 8.9990 chunk 112 optimal weight: 0.0270 overall best weight: 2.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 268 ASN ** F 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.119834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.083069 restraints weight = 117186.498| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 5.59 r_work: 0.3112 rms_B_bonded: 5.24 restraints_weight: 2.0000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3106 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3106 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 22467 Z= 0.185 Angle : 0.718 14.363 30782 Z= 0.361 Chirality : 0.044 0.219 3565 Planarity : 0.005 0.085 3731 Dihedral : 14.027 124.225 3851 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.29 % Favored : 89.48 % Rotamer: Outliers : 6.75 % Allowed : 26.29 % Favored : 66.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.34 (0.15), residues: 2639 helix: -0.78 (0.17), residues: 917 sheet: -3.67 (0.28), residues: 237 loop : -3.04 (0.14), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP G 53 HIS 0.008 0.001 HIS F 33 PHE 0.030 0.002 PHE F 357 TYR 0.028 0.002 TYR F 306 ARG 0.005 0.001 ARG B 75 Details of bonding type rmsd hydrogen bonds : bond 0.06026 ( 701) hydrogen bonds : angle 5.55725 ( 1937) metal coordination : bond 0.01823 ( 32) metal coordination : angle 5.13012 ( 28) covalent geometry : bond 0.00420 (22434) covalent geometry : angle 0.70113 (30754) Misc. bond : bond 0.00064 ( 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 284 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 132 time to evaluate : 2.373 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: 0.9016 (OUTLIER) cc_final: 0.8797 (pp) REVERT: A 478 LYS cc_start: 0.9078 (OUTLIER) cc_final: 0.8872 (ttmm) REVERT: A 553 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7748 (ptm-80) REVERT: A 735 ARG cc_start: 0.7112 (OUTLIER) cc_final: 0.6574 (mtm-85) REVERT: A 802 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.7733 (mp0) REVERT: A 906 MET cc_start: 0.6933 (OUTLIER) cc_final: 0.6221 (mmm) REVERT: A 917 GLU cc_start: 0.9048 (OUTLIER) cc_final: 0.8749 (mt-10) REVERT: B 48 GLU cc_start: 0.8689 (tt0) cc_final: 0.8321 (tt0) REVERT: B 65 GLN cc_start: 0.8763 (tm-30) cc_final: 0.8517 (tm-30) REVERT: B 77 GLU cc_start: 0.8867 (tp30) cc_final: 0.8610 (tp30) REVERT: B 94 MET cc_start: 0.8722 (ttp) cc_final: 0.8518 (ttp) REVERT: C 34 GLN cc_start: 0.8861 (tp40) cc_final: 0.8001 (tp-100) REVERT: C 38 ASP cc_start: 0.8296 (m-30) cc_final: 0.7631 (m-30) REVERT: C 52 MET cc_start: 0.8954 (tpp) cc_final: 0.8746 (tpt) REVERT: F 65 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8860 (tt) REVERT: F 233 MET cc_start: 0.8596 (mmm) cc_final: 0.8381 (mmm) REVERT: F 325 LEU cc_start: 0.3340 (OUTLIER) cc_final: 0.2204 (tp) REVERT: E 277 TYR cc_start: 0.6790 (OUTLIER) cc_final: 0.6123 (p90) REVERT: E 436 MET cc_start: 0.7653 (mmt) cc_final: 0.7437 (mmt) REVERT: E 541 TYR cc_start: 0.7990 (t80) cc_final: 0.7651 (t80) REVERT: G 53 TRP cc_start: 0.7338 (m100) cc_final: 0.7118 (m100) REVERT: G 58 LYS cc_start: 0.8896 (tptp) cc_final: 0.8576 (tptp) REVERT: G 87 TYR cc_start: 0.7842 (m-80) cc_final: 0.7566 (m-80) REVERT: G 111 ARG cc_start: 0.7546 (mmm160) cc_final: 0.7198 (mmm160) outliers start: 152 outliers final: 96 residues processed: 269 average time/residue: 0.3276 time to fit residues: 138.3936 Evaluate side-chains 228 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 122 time to evaluate : 2.328 ------------------------------------------------------------------------------- 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 86 ILE 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 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 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 435 VAL 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 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 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 883 LEU 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 83 VAL Chi-restraints excluded: chain B residue 85 SER 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 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 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 42 LEU 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 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 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 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 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 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 219 LEU 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 424 SER Chi-restraints excluded: chain E residue 462 LYS Chi-restraints excluded: chain G residue 21 THR 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 101 optimal weight: 7.9990 chunk 63 optimal weight: 2.9990 chunk 252 optimal weight: 0.9980 chunk 108 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 118 optimal weight: 6.9990 chunk 156 optimal weight: 6.9990 chunk 64 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 256 optimal weight: 9.9990 chunk 181 optimal weight: 20.0000 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 519 ASN ** E 75 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.119766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.082948 restraints weight = 117405.069| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 5.52 r_work: 0.3114 rms_B_bonded: 5.21 restraints_weight: 2.0000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3085 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3085 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.118 22467 Z= 0.191 Angle : 0.718 14.391 30782 Z= 0.358 Chirality : 0.043 0.219 3565 Planarity : 0.005 0.079 3731 Dihedral : 13.723 124.514 3839 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.75 % Favored : 89.02 % Rotamer: Outliers : 6.18 % Allowed : 27.39 % Favored : 66.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.19 (0.15), residues: 2639 helix: -0.68 (0.17), residues: 919 sheet: -3.47 (0.28), residues: 258 loop : -2.92 (0.14), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 916 HIS 0.008 0.001 HIS F 33 PHE 0.028 0.002 PHE F 357 TYR 0.030 0.002 TYR B 135 ARG 0.005 0.001 ARG G 39 Details of bonding type rmsd hydrogen bonds : bond 0.05981 ( 701) hydrogen bonds : angle 5.41345 ( 1937) metal coordination : bond 0.03033 ( 32) metal coordination : angle 5.25768 ( 28) covalent geometry : bond 0.00433 (22434) covalent geometry : angle 0.70014 (30754) Misc. bond : bond 0.00073 ( 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 264 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 125 time to evaluate : 2.363 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 366 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8793 (pp) REVERT: A 478 LYS cc_start: 0.9087 (OUTLIER) cc_final: 0.8878 (ttmm) REVERT: A 607 SER cc_start: 0.9325 (OUTLIER) cc_final: 0.9001 (p) REVERT: A 657 ASN cc_start: 0.8660 (OUTLIER) cc_final: 0.8381 (t0) REVERT: A 735 ARG cc_start: 0.7160 (OUTLIER) cc_final: 0.6622 (mtm-85) REVERT: A 802 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.7731 (mp0) REVERT: A 857 GLU cc_start: 0.8311 (tp30) cc_final: 0.8049 (tp30) REVERT: A 899 MET cc_start: 0.7785 (ttp) cc_final: 0.7524 (ttp) REVERT: A 906 MET cc_start: 0.6972 (mmm) cc_final: 0.6647 (mmm) REVERT: A 917 GLU cc_start: 0.9073 (OUTLIER) cc_final: 0.8846 (mp0) REVERT: B 48 GLU cc_start: 0.8703 (tt0) cc_final: 0.8341 (tt0) REVERT: B 65 GLN cc_start: 0.8765 (tm-30) cc_final: 0.8479 (tm-30) REVERT: B 77 GLU cc_start: 0.8853 (tp30) cc_final: 0.8592 (tp30) REVERT: C 21 ARG cc_start: 0.8969 (mmm160) cc_final: 0.8719 (mmm160) REVERT: C 34 GLN cc_start: 0.8868 (tp40) cc_final: 0.7985 (tp-100) REVERT: C 38 ASP cc_start: 0.8317 (m-30) cc_final: 0.7636 (m-30) REVERT: C 52 MET cc_start: 0.8989 (tpp) cc_final: 0.8763 (tpt) REVERT: F 65 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.8965 (tt) REVERT: F 233 MET cc_start: 0.8644 (mmm) cc_final: 0.8431 (mmm) REVERT: F 325 LEU cc_start: 0.3886 (OUTLIER) cc_final: 0.2823 (tp) REVERT: E 260 ASP cc_start: 0.6546 (OUTLIER) cc_final: 0.5412 (m-30) REVERT: E 277 TYR cc_start: 0.6636 (OUTLIER) cc_final: 0.6147 (p90) REVERT: E 436 MET cc_start: 0.7660 (mmt) cc_final: 0.7443 (mmt) REVERT: E 541 TYR cc_start: 0.8000 (t80) cc_final: 0.7688 (t80) REVERT: G 58 LYS cc_start: 0.8852 (tptp) cc_final: 0.8494 (tptp) REVERT: G 111 ARG cc_start: 0.7598 (mmm160) cc_final: 0.7179 (mmm160) outliers start: 139 outliers final: 103 residues processed: 252 average time/residue: 0.3176 time to fit residues: 126.8231 Evaluate side-chains 234 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 120 time to evaluate : 2.514 ------------------------------------------------------------------------------- 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 86 ILE Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 178 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 366 LEU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 435 VAL 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 657 ASN Chi-restraints excluded: chain A residue 675 VAL 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 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 883 LEU Chi-restraints excluded: chain A residue 892 HIS Chi-restraints excluded: chain A residue 900 LEU 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 83 VAL Chi-restraints excluded: chain B residue 85 SER 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 98 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 132 ILE 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 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 78 ASP 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 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 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 340 VAL 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 F residue 563 VAL Chi-restraints excluded: chain E residue 60 VAL 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 219 LEU 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 388 ASN Chi-restraints excluded: chain E residue 424 SER Chi-restraints excluded: chain E residue 462 LYS 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 110 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 96 optimal weight: 9.9990 chunk 234 optimal weight: 8.9990 chunk 134 optimal weight: 2.9990 chunk 212 optimal weight: 9.9990 chunk 99 optimal weight: 0.9980 chunk 185 optimal weight: 7.9990 chunk 114 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 66 optimal weight: 0.0000 chunk 0 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.130722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.085779 restraints weight = 92684.499| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 6.42 r_work: 0.3257 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3340 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3340 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 22467 Z= 0.158 Angle : 0.688 13.784 30782 Z= 0.343 Chirality : 0.042 0.218 3565 Planarity : 0.004 0.078 3731 Dihedral : 13.409 124.196 3822 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.03 % Favored : 89.78 % Rotamer: Outliers : 6.04 % Allowed : 27.00 % Favored : 66.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.15), residues: 2639 helix: -0.50 (0.17), residues: 918 sheet: -3.38 (0.27), residues: 264 loop : -2.81 (0.15), residues: 1457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 53 HIS 0.009 0.001 HIS F 33 PHE 0.028 0.001 PHE F 357 TYR 0.034 0.002 TYR A 903 ARG 0.005 0.000 ARG B 75 Details of bonding type rmsd hydrogen bonds : bond 0.05694 ( 701) hydrogen bonds : angle 5.21158 ( 1937) metal coordination : bond 0.02708 ( 32) metal coordination : angle 4.92897 ( 28) covalent geometry : bond 0.00354 (22434) covalent geometry : angle 0.67194 (30754) Misc. bond : bond 0.00056 ( 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 263 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 127 time to evaluate : 2.396 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 366 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8767 (pp) REVERT: A 478 LYS cc_start: 0.9090 (OUTLIER) cc_final: 0.8837 (ttmm) REVERT: A 735 ARG cc_start: 0.7120 (OUTLIER) cc_final: 0.6555 (mtm-85) REVERT: A 802 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7668 (mp0) REVERT: B 48 GLU cc_start: 0.8647 (tt0) cc_final: 0.8351 (tt0) REVERT: B 65 GLN cc_start: 0.8711 (tm-30) cc_final: 0.8480 (tm-30) REVERT: B 77 GLU cc_start: 0.8839 (tp30) cc_final: 0.8616 (tp30) REVERT: B 157 GLN cc_start: 0.8329 (pp30) cc_final: 0.8030 (pp30) REVERT: C 34 GLN cc_start: 0.8902 (tp40) cc_final: 0.8062 (tp-100) REVERT: C 38 ASP cc_start: 0.8258 (m-30) cc_final: 0.7690 (m-30) REVERT: D 129 MET cc_start: 0.8163 (OUTLIER) cc_final: 0.7457 (mmm) REVERT: F 65 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.8950 (tt) REVERT: F 233 MET cc_start: 0.8730 (mmm) cc_final: 0.8490 (mmm) REVERT: F 325 LEU cc_start: 0.3115 (OUTLIER) cc_final: 0.1991 (tp) REVERT: E 277 TYR cc_start: 0.6521 (OUTLIER) cc_final: 0.5949 (p90) REVERT: E 436 MET cc_start: 0.7551 (mmt) cc_final: 0.7298 (mmt) REVERT: E 541 TYR cc_start: 0.8041 (t80) cc_final: 0.7611 (t80) REVERT: G 58 LYS cc_start: 0.8826 (tptp) cc_final: 0.8431 (tptp) REVERT: G 111 ARG cc_start: 0.7753 (mmm160) cc_final: 0.7276 (mmm160) outliers start: 136 outliers final: 104 residues processed: 252 average time/residue: 0.3033 time to fit residues: 121.8078 Evaluate side-chains 233 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 121 time to evaluate : 2.318 ------------------------------------------------------------------------------- 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 86 ILE Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 138 ASN 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 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 366 LEU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 377 ASP Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 435 VAL 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 768 SER Chi-restraints excluded: chain A residue 772 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 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 85 SER 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 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 64 ASP Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 83 VAL 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 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 141 THR 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 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 E residue 60 VAL 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 301 SER Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 387 VAL Chi-restraints excluded: chain E residue 424 SER Chi-restraints excluded: chain E residue 462 LYS 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 110 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 203 optimal weight: 10.0000 chunk 194 optimal weight: 40.0000 chunk 236 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 chunk 29 optimal weight: 0.0270 chunk 229 optimal weight: 20.0000 chunk 128 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 265 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 167 optimal weight: 5.9990 overall best weight: 2.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 ASN D 109 ASN ** F 62 GLN ** 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 470 GLN G 33 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.119013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.077521 restraints weight = 83969.176| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 4.80 r_work: 0.3130 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3130 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3130 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 22467 Z= 0.221 Angle : 0.723 14.715 30782 Z= 0.362 Chirality : 0.044 0.219 3565 Planarity : 0.004 0.073 3731 Dihedral : 13.368 124.892 3814 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.19 % Allowed : 11.01 % Favored : 88.80 % Rotamer: Outliers : 6.22 % Allowed : 27.35 % Favored : 66.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.15), residues: 2639 helix: -0.54 (0.17), residues: 920 sheet: -3.16 (0.30), residues: 234 loop : -2.73 (0.15), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP G 53 HIS 0.009 0.001 HIS F 33 PHE 0.035 0.002 PHE F 357 TYR 0.050 0.002 TYR F 306 ARG 0.005 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.06035 ( 701) hydrogen bonds : angle 5.29880 ( 1937) metal coordination : bond 0.02577 ( 32) metal coordination : angle 4.97369 ( 28) covalent geometry : bond 0.00507 (22434) covalent geometry : angle 0.70755 (30754) Misc. bond : bond 0.00100 ( 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 264 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 124 time to evaluate : 2.325 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 366 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8792 (pp) REVERT: A 553 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7734 (ptm-80) REVERT: A 607 SER cc_start: 0.9281 (OUTLIER) cc_final: 0.8966 (p) REVERT: A 657 ASN cc_start: 0.8730 (OUTLIER) cc_final: 0.8428 (t0) REVERT: A 735 ARG cc_start: 0.7141 (OUTLIER) cc_final: 0.6592 (mtm-85) REVERT: A 802 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.7650 (mp0) REVERT: B 65 GLN cc_start: 0.8736 (tm-30) cc_final: 0.8442 (tm-30) REVERT: B 77 GLU cc_start: 0.8777 (tp30) cc_final: 0.8529 (tp30) REVERT: B 168 GLN cc_start: 0.8534 (mp10) cc_final: 0.8275 (mp10) REVERT: C 34 GLN cc_start: 0.8817 (tp40) cc_final: 0.7887 (tp-100) REVERT: C 38 ASP cc_start: 0.8213 (m-30) cc_final: 0.7554 (m-30) REVERT: D 129 MET cc_start: 0.8142 (OUTLIER) cc_final: 0.7380 (mmm) REVERT: F 65 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.8876 (tt) REVERT: F 233 MET cc_start: 0.8734 (mmm) cc_final: 0.8488 (mmm) REVERT: F 325 LEU cc_start: 0.3336 (OUTLIER) cc_final: 0.2202 (tp) REVERT: E 260 ASP cc_start: 0.6497 (OUTLIER) cc_final: 0.5299 (m-30) REVERT: E 436 MET cc_start: 0.7550 (mmt) cc_final: 0.7245 (mmt) REVERT: E 541 TYR cc_start: 0.8053 (t80) cc_final: 0.7680 (t80) REVERT: G 58 LYS cc_start: 0.8771 (tptp) cc_final: 0.8374 (tptp) REVERT: G 111 ARG cc_start: 0.7649 (mmm160) cc_final: 0.7229 (mmm160) outliers start: 140 outliers final: 108 residues processed: 254 average time/residue: 0.3092 time to fit residues: 124.8334 Evaluate side-chains 239 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 121 time to evaluate : 2.306 ------------------------------------------------------------------------------- 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 86 ILE Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 178 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 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 366 LEU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 377 ASP 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 435 VAL Chi-restraints excluded: chain A residue 495 VAL 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 657 ASN Chi-restraints excluded: chain A residue 675 VAL 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 768 SER Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 776 VAL 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 68 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 85 SER 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 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 78 ASP Chi-restraints excluded: chain D residue 83 VAL 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 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 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 432 ILE 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 526 LEU 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 61 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 424 SER Chi-restraints excluded: chain E residue 462 LYS 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 59 SER 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 258 optimal weight: 9.9990 chunk 180 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 134 optimal weight: 0.0370 chunk 150 optimal weight: 9.9990 chunk 31 optimal weight: 0.9990 chunk 195 optimal weight: 0.0020 chunk 210 optimal weight: 9.9990 chunk 72 optimal weight: 0.5980 chunk 172 optimal weight: 3.9990 overall best weight: 0.5268 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 95 ASN F 395 HIS ** F 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.132740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.090513 restraints weight = 119014.776| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 6.97 r_work: 0.3378 rms_B_bonded: 6.01 restraints_weight: 2.0000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3380 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3380 r_free = 0.3380 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3380 r_free = 0.3380 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3380 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 22467 Z= 0.118 Angle : 0.664 12.406 30782 Z= 0.329 Chirality : 0.041 0.215 3565 Planarity : 0.004 0.076 3731 Dihedral : 13.090 123.616 3812 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.43 % Favored : 91.38 % Rotamer: Outliers : 4.41 % Allowed : 29.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.16), residues: 2639 helix: -0.23 (0.17), residues: 925 sheet: -2.98 (0.32), residues: 211 loop : -2.62 (0.15), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP G 53 HIS 0.007 0.001 HIS F 33 PHE 0.036 0.001 PHE F 357 TYR 0.049 0.001 TYR F 306 ARG 0.007 0.001 ARG G 39 Details of bonding type rmsd hydrogen bonds : bond 0.05304 ( 701) hydrogen bonds : angle 4.88569 ( 1937) metal coordination : bond 0.01980 ( 32) metal coordination : angle 4.71476 ( 28) covalent geometry : bond 0.00247 (22434) covalent geometry : angle 0.64868 (30754) Misc. bond : bond 0.00018 ( 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 240 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 141 time to evaluate : 2.389 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 141 THR cc_start: 0.8731 (OUTLIER) cc_final: 0.8490 (m) REVERT: A 657 ASN cc_start: 0.8724 (OUTLIER) cc_final: 0.8471 (t0) REVERT: A 735 ARG cc_start: 0.7171 (OUTLIER) cc_final: 0.6547 (mtm-85) REVERT: A 802 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7702 (mp0) REVERT: B 65 GLN cc_start: 0.8720 (tm-30) cc_final: 0.8454 (tm-30) REVERT: B 80 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.8392 (ttt180) REVERT: B 157 GLN cc_start: 0.8379 (pp30) cc_final: 0.8065 (pp30) REVERT: B 168 GLN cc_start: 0.8621 (mp10) cc_final: 0.8385 (mp10) REVERT: C 34 GLN cc_start: 0.8931 (tp40) cc_final: 0.8156 (tp-100) REVERT: C 38 ASP cc_start: 0.8338 (m-30) cc_final: 0.7784 (m-30) REVERT: D 12 TYR cc_start: 0.8600 (t80) cc_final: 0.8335 (t80) REVERT: D 129 MET cc_start: 0.8158 (OUTLIER) cc_final: 0.7467 (mmm) REVERT: F 65 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8689 (tt) REVERT: F 233 MET cc_start: 0.8806 (mmm) cc_final: 0.8585 (mmm) REVERT: F 288 LYS cc_start: 0.7324 (OUTLIER) cc_final: 0.7034 (mtmm) REVERT: E 436 MET cc_start: 0.7623 (mmt) cc_final: 0.7354 (mmt) REVERT: E 541 TYR cc_start: 0.7983 (t80) cc_final: 0.7651 (t80) REVERT: G 58 LYS cc_start: 0.8895 (tptp) cc_final: 0.8603 (tptp) REVERT: G 87 TYR cc_start: 0.7874 (m-80) cc_final: 0.7310 (m-80) REVERT: G 89 TYR cc_start: 0.5522 (m-10) cc_final: 0.4686 (m-80) REVERT: G 111 ARG cc_start: 0.7768 (mmm160) cc_final: 0.7302 (mmm160) outliers start: 99 outliers final: 68 residues processed: 234 average time/residue: 0.3279 time to fit residues: 120.3213 Evaluate side-chains 204 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 128 time to evaluate : 2.511 ------------------------------------------------------------------------------- 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 141 THR 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 278 GLU 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 401 LEU Chi-restraints excluded: chain A residue 482 CYS 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 734 ASN Chi-restraints excluded: chain A residue 735 ARG Chi-restraints excluded: chain A residue 768 SER Chi-restraints excluded: chain A residue 772 SER Chi-restraints excluded: chain A residue 776 VAL 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 41 SER 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 C residue 43 LYS 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 42 LEU Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 77 GLU 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 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 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 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 563 VAL Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain E residue 185 TYR Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 356 VAL 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 59 SER Chi-restraints excluded: chain G residue 79 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 13 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 172 optimal weight: 0.0470 chunk 157 optimal weight: 4.9990 chunk 140 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 256 optimal weight: 20.0000 chunk 254 optimal weight: 0.6980 overall best weight: 0.7282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 898 HIS D 104 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 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 423 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 = 0.4519 r_free = 0.4519 target = 0.133245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.089754 restraints weight = 119606.503| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 6.83 r_work: 0.3387 rms_B_bonded: 5.14 restraints_weight: 2.0000 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3388 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3388 r_free = 0.3388 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3388 r_free = 0.3388 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3388 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 22467 Z= 0.118 Angle : 0.661 11.745 30782 Z= 0.326 Chirality : 0.041 0.215 3565 Planarity : 0.004 0.072 3731 Dihedral : 12.796 124.030 3791 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.85 % Favored : 90.96 % Rotamer: Outliers : 3.53 % Allowed : 30.26 % Favored : 66.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.16), residues: 2639 helix: -0.03 (0.17), residues: 925 sheet: -2.81 (0.31), residues: 237 loop : -2.55 (0.15), residues: 1477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 53 HIS 0.010 0.001 HIS A 898 PHE 0.028 0.001 PHE F 357 TYR 0.035 0.001 TYR A 903 ARG 0.007 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.05175 ( 701) hydrogen bonds : angle 4.76730 ( 1937) metal coordination : bond 0.01839 ( 32) metal coordination : angle 4.42691 ( 28) covalent geometry : bond 0.00260 (22434) covalent geometry : angle 0.64744 (30754) Misc. bond : bond 0.00031 ( 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 213 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 134 time to evaluate : 2.532 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: 0.8748 (OUTLIER) cc_final: 0.8524 (t0) REVERT: A 735 ARG cc_start: 0.7110 (OUTLIER) cc_final: 0.6522 (mtm-85) REVERT: A 802 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7799 (mp0) REVERT: B 65 GLN cc_start: 0.8663 (tm-30) cc_final: 0.8407 (tm-30) REVERT: B 80 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.8327 (ttt180) REVERT: B 157 GLN cc_start: 0.8304 (pp30) cc_final: 0.7989 (pp30) REVERT: C 34 GLN cc_start: 0.8877 (tp40) cc_final: 0.8061 (tp-100) REVERT: C 38 ASP cc_start: 0.8295 (m-30) cc_final: 0.7729 (m-30) REVERT: D 12 TYR cc_start: 0.8573 (t80) cc_final: 0.8332 (t80) REVERT: D 129 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.7427 (mmm) REVERT: F 68 MET cc_start: 0.7680 (mmm) cc_final: 0.7469 (mmp) REVERT: F 233 MET cc_start: 0.8868 (mmm) cc_final: 0.8628 (mmm) REVERT: E 429 MET cc_start: 0.8223 (mtm) cc_final: 0.7897 (mtm) REVERT: E 436 MET cc_start: 0.7474 (mmt) cc_final: 0.7169 (mmt) REVERT: E 462 LYS cc_start: 0.3510 (OUTLIER) cc_final: 0.2984 (mtmm) REVERT: E 541 TYR cc_start: 0.8015 (t80) cc_final: 0.7645 (t80) REVERT: G 58 LYS cc_start: 0.8723 (tptp) cc_final: 0.8408 (tptp) REVERT: G 87 TYR cc_start: 0.7801 (m-80) cc_final: 0.7524 (m-80) REVERT: G 89 TYR cc_start: 0.5526 (m-10) cc_final: 0.4796 (m-80) REVERT: G 111 ARG cc_start: 0.7729 (mmm160) cc_final: 0.7279 (mmm160) outliers start: 79 outliers final: 64 residues processed: 207 average time/residue: 0.3355 time to fit residues: 109.3850 Evaluate side-chains 193 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 123 time to evaluate : 2.434 ------------------------------------------------------------------------------- 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 206 THR Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 278 GLU 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 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 734 ASN Chi-restraints excluded: chain A residue 735 ARG 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 858 ARG Chi-restraints excluded: chain A residue 892 HIS 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 C residue 43 LYS 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 83 VAL 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 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 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 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 563 VAL Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain E residue 154 VAL 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 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 59 SER 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 139 optimal weight: 0.0020 chunk 46 optimal weight: 0.9980 chunk 43 optimal weight: 0.0970 chunk 55 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 208 optimal weight: 4.9990 chunk 154 optimal weight: 5.9990 chunk 181 optimal weight: 10.0000 chunk 91 optimal weight: 0.8980 chunk 188 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 95 ASN ** F 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.132855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.090724 restraints weight = 131552.042| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 6.77 r_work: 0.3388 rms_B_bonded: 5.11 restraints_weight: 2.0000 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3384 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3384 r_free = 0.3384 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3384 r_free = 0.3384 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3384 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.4038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 22467 Z= 0.134 Angle : 0.674 15.899 30782 Z= 0.330 Chirality : 0.041 0.215 3565 Planarity : 0.004 0.073 3731 Dihedral : 12.737 124.297 3783 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.04 % Favored : 90.81 % Rotamer: Outliers : 3.35 % Allowed : 30.44 % Favored : 66.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.16), residues: 2639 helix: -0.03 (0.17), residues: 925 sheet: -2.70 (0.30), residues: 249 loop : -2.50 (0.15), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 53 HIS 0.008 0.001 HIS F 33 PHE 0.024 0.001 PHE F 357 TYR 0.032 0.001 TYR F 306 ARG 0.007 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.05243 ( 701) hydrogen bonds : angle 4.74882 ( 1937) metal coordination : bond 0.01902 ( 32) metal coordination : angle 4.47620 ( 28) covalent geometry : bond 0.00301 (22434) covalent geometry : angle 0.66037 (30754) Misc. bond : bond 0.00056 ( 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 205 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 130 time to evaluate : 2.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 657 ASN cc_start: 0.8746 (OUTLIER) cc_final: 0.8539 (t0) REVERT: A 735 ARG cc_start: 0.7143 (OUTLIER) cc_final: 0.6557 (mtm-85) REVERT: A 802 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7770 (mp0) REVERT: B 57 ARG cc_start: 0.8531 (ttp-110) cc_final: 0.8277 (ttp-110) REVERT: B 65 GLN cc_start: 0.8633 (tm-30) cc_final: 0.8403 (tm-30) REVERT: B 80 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.8336 (ttt180) REVERT: B 157 GLN cc_start: 0.8355 (pp30) cc_final: 0.8040 (pp30) REVERT: C 34 GLN cc_start: 0.8917 (tp40) cc_final: 0.8112 (tp-100) REVERT: C 38 ASP cc_start: 0.8345 (m-30) cc_final: 0.7796 (m-30) REVERT: D 129 MET cc_start: 0.8191 (OUTLIER) cc_final: 0.7471 (mmm) REVERT: F 65 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.8965 (tt) REVERT: F 233 MET cc_start: 0.8843 (mmm) cc_final: 0.8565 (mmm) REVERT: E 429 MET cc_start: 0.8074 (mtm) cc_final: 0.7679 (mtm) REVERT: E 436 MET cc_start: 0.7236 (mmt) cc_final: 0.6918 (mmt) REVERT: E 462 LYS cc_start: 0.3256 (OUTLIER) cc_final: 0.2582 (mtmm) REVERT: E 541 TYR cc_start: 0.8054 (t80) cc_final: 0.7503 (t80) REVERT: G 58 LYS cc_start: 0.8704 (tptp) cc_final: 0.8316 (tptp) REVERT: G 87 TYR cc_start: 0.7751 (m-80) cc_final: 0.7467 (m-80) REVERT: G 89 TYR cc_start: 0.5775 (m-80) cc_final: 0.5033 (m-80) REVERT: G 111 ARG cc_start: 0.7716 (mmm160) cc_final: 0.7292 (mmm160) outliers start: 75 outliers final: 66 residues processed: 202 average time/residue: 0.3409 time to fit residues: 107.5609 Evaluate side-chains 197 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 124 time to evaluate : 2.485 ------------------------------------------------------------------------------- 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 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 295 HIS Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 482 CYS 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 734 ASN Chi-restraints excluded: chain A residue 735 ARG 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 858 ARG Chi-restraints excluded: chain A residue 892 HIS Chi-restraints excluded: chain B residue 41 SER 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 64 ASP Chi-restraints excluded: chain D residue 83 VAL 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 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 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 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 563 VAL Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 301 SER 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 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 59 SER 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 0 optimal weight: 6.9990 chunk 123 optimal weight: 5.9990 chunk 244 optimal weight: 30.0000 chunk 206 optimal weight: 5.9990 chunk 215 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 chunk 189 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 115 optimal weight: 0.0170 chunk 116 optimal weight: 7.9990 chunk 214 optimal weight: 20.0000 overall best weight: 3.4024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 898 HIS ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 ASN ** 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 268 ASN E 349 ASN ** E 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.118597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.081374 restraints weight = 120996.041| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 5.51 r_work: 0.3098 rms_B_bonded: 5.33 restraints_weight: 2.0000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3070 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3070 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 22467 Z= 0.273 Angle : 0.774 15.339 30782 Z= 0.384 Chirality : 0.045 0.230 3565 Planarity : 0.005 0.070 3731 Dihedral : 12.960 126.120 3783 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.33 % Favored : 89.52 % Rotamer: Outliers : 3.66 % Allowed : 30.39 % Favored : 65.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.16), residues: 2639 helix: -0.39 (0.17), residues: 922 sheet: -3.00 (0.29), residues: 257 loop : -2.50 (0.15), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 53 HIS 0.010 0.001 HIS F 33 PHE 0.021 0.002 PHE F 357 TYR 0.042 0.002 TYR D 12 ARG 0.007 0.001 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.06274 ( 701) hydrogen bonds : angle 5.18993 ( 1937) metal coordination : bond 0.02406 ( 32) metal coordination : angle 5.09512 ( 28) covalent geometry : bond 0.00629 (22434) covalent geometry : angle 0.75873 (30754) Misc. bond : bond 0.00126 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16772.97 seconds wall clock time: 289 minutes 53.47 seconds (17393.47 seconds total)