Starting phenix.real_space_refine on Mon Aug 10 07:45:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9s29_54482/08_2026/9s29_54482.cif Found real_map, /net/cci-nas-00/data/ceres_data/9s29_54482/08_2026/9s29_54482.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9s29_54482/08_2026/9s29_54482.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9s29_54482/08_2026/9s29_54482.map" model { file = "/net/cci-nas-00/data/ceres_data/9s29_54482/08_2026/9s29_54482.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9s29_54482/08_2026/9s29_54482.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 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 16 6.06 5 P 78 5.49 5 S 216 5.16 5 C 27268 2.51 5 N 7668 2.21 5 O 8190 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 43436 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 2223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2223 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 14, 'TRANS': 261} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2038 Classifications: {'peptide': 252} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 241} Chain breaks: 2 Chain: "C" Number of atoms: 2150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2150 Classifications: {'peptide': 265} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 252} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 2132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2132 Classifications: {'peptide': 263} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 249} Chain breaks: 1 Chain: "E" Number of atoms: 2180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2180 Classifications: {'peptide': 269} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 254} Chain breaks: 1 Chain: "F" Number of atoms: 2136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2136 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 253} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'TRP:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "G" Number of atoms: 2010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 2010 Classifications: {'peptide': 247} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 236} Chain breaks: 4 Chain: "H" Number of atoms: 2136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2136 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 13, 'TRANS': 250} Chain breaks: 2 Chain: "W" Number of atoms: 428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 428 Classifications: {'DNA': 21} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 20} Chain: "X" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 389 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "a" Number of atoms: 654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 654 Classifications: {'peptide': 80} Link IDs: {'TRANS': 79} Chain: "b" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 644 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 79} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "c" Number of atoms: 654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 654 Classifications: {'peptide': 80} Link IDs: {'TRANS': 79} Chain: "d" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 646 Classifications: {'peptide': 79} Link IDs: {'TRANS': 78} Chain: "e" Number of atoms: 654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 654 Classifications: {'peptide': 80} Link IDs: {'TRANS': 79} Chain: "f" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 636 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 78} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "I" Number of atoms: 2223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2223 Classifications: {'peptide': 276} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 14, 'TRANS': 261} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 2038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2038 Classifications: {'peptide': 252} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 241} Chain breaks: 2 Chain: "K" Number of atoms: 2150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2150 Classifications: {'peptide': 265} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 252} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 2132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2132 Classifications: {'peptide': 263} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 249} Chain breaks: 1 Chain: "M" Number of atoms: 2180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2180 Classifications: {'peptide': 269} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 254} Chain breaks: 1 Chain: "N" Number of atoms: 2136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2136 Classifications: {'peptide': 267} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 253} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'TRP:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "O" Number of atoms: 2010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 2010 Classifications: {'peptide': 247} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 236} Chain breaks: 4 Chain: "P" Number of atoms: 2136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2136 Classifications: {'peptide': 264} Link IDs: {'PTRANS': 13, 'TRANS': 250} Chain breaks: 2 Chain: "Y" Number of atoms: 428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 428 Classifications: {'DNA': 21} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 20} Chain: "Z" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 389 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Chain: "g" Number of atoms: 654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 654 Classifications: {'peptide': 80} Link IDs: {'TRANS': 79} Chain: "h" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 644 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 79} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "i" Number of atoms: 654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 654 Classifications: {'peptide': 80} Link IDs: {'TRANS': 79} Chain: "j" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 646 Classifications: {'peptide': 79} Link IDs: {'TRANS': 78} Chain: "k" Number of atoms: 654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 654 Classifications: {'peptide': 80} Link IDs: {'TRANS': 79} Chain: "l" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 636 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 78} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 329 SG CYS A 40 128.502 124.499 48.378 1.00 36.16 S ATOM 350 SG CYS A 43 125.247 122.395 48.938 1.00 29.78 S ATOM 2538 SG CYS B 40 37.630 141.306 66.931 1.00163.97 S ATOM 2559 SG CYS B 43 39.314 143.136 63.973 1.00156.80 S ATOM 4590 SG CYS C 40 68.354 165.142 39.123 1.00 19.61 S ATOM 4611 SG CYS C 43 65.352 163.361 40.830 1.00 19.40 S ATOM 6726 SG CYS D 40 49.736 196.652 69.049 1.00 48.45 S ATOM 6747 SG CYS D 43 49.832 194.232 72.056 1.00 57.60 S ATOM 8872 SG CYS E 40 146.231 133.224 74.398 1.00 58.91 S ATOM 8893 SG CYS E 43 144.244 135.394 76.982 1.00 72.98 S ATOM 11039 SG CYS F 40 128.405 166.428 39.431 1.00 76.45 S ATOM 11060 SG CYS F 43 131.392 168.291 41.033 1.00 86.86 S ATOM 13188 SG CYS G 40 152.725 190.011 77.838 1.00114.30 S ATOM 13209 SG CYS G 43 152.219 188.094 74.494 1.00113.97 S ATOM 15184 SG CYS H 40 120.831 220.380 53.968 1.00212.97 S ATOM 15205 SG CYS H 43 118.302 217.552 54.748 1.00207.78 S ATOM 22039 SG CYS I 40 69.097 109.200 48.379 1.00 34.52 S ATOM 22060 SG CYS I 43 72.350 111.308 48.937 1.00 28.77 S ATOM 24248 SG CYS J 40 159.982 92.410 66.954 1.00167.90 S ATOM 24269 SG CYS J 43 158.312 90.581 63.988 1.00160.41 S ATOM 26300 SG CYS K 40 129.250 68.551 39.117 1.00 21.21 S ATOM 26321 SG CYS K 43 132.238 70.335 40.845 1.00 17.95 S ATOM 28436 SG CYS L 40 147.916 37.079 69.087 1.00 53.24 S ATOM 28457 SG CYS L 43 147.818 39.499 72.095 1.00 61.40 S ATOM 30582 SG CYS M 40 51.369 100.476 74.387 1.00 55.89 S ATOM 30603 SG CYS M 43 53.370 98.324 76.977 1.00 73.99 S ATOM 32749 SG CYS N 40 69.243 67.289 39.454 1.00153.18 S ATOM 32770 SG CYS N 43 66.252 65.429 41.056 1.00158.42 S ATOM 34898 SG CYS O 40 44.909 43.691 77.867 1.00112.41 S ATOM 34919 SG CYS O 43 45.419 45.614 74.524 1.00107.70 S ATOM 36894 SG CYS P 40 76.826 13.335 53.998 1.00209.66 S ATOM 36915 SG CYS P 43 79.352 16.164 54.781 1.00207.71 S Time building chain proxies: 12.33, per 1000 atoms: 0.28 Number of scatterers: 43436 At special positions: 0 Unit cell: (198.55, 234.65, 112.1, 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 16 29.99 S 216 16.00 P 78 15.00 O 8190 8.00 N 7668 7.00 C 27268 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.60 Conformation dependent library (CDL) restraints added in 1.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" ND1 HIS A 16 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 12 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 43 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 40 " pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" ND1 HIS B 16 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 12 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 40 " pdb="ZN ZN B 301 " - pdb=" SG CYS B 43 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 40 " pdb="ZN ZN C 301 " - pdb=" NE2 HIS C 12 " pdb="ZN ZN C 301 " - pdb=" ND1 HIS C 16 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 43 " pdb=" ZN D 301 " pdb="ZN ZN D 301 " - pdb=" ND1 HIS D 16 " pdb="ZN ZN D 301 " - pdb=" NE2 HIS D 12 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 43 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 40 " pdb=" ZN E 301 " pdb="ZN ZN E 301 " - pdb=" ND1 HIS E 16 " pdb="ZN ZN E 301 " - pdb=" NE2 HIS E 12 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 43 " pdb="ZN ZN E 301 " - pdb=" SG CYS E 40 " pdb=" ZN F 301 " pdb="ZN ZN F 301 " - pdb=" NE2 HIS F 12 " pdb="ZN ZN F 301 " - pdb=" ND1 HIS F 16 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 40 " pdb="ZN ZN F 301 " - pdb=" SG CYS F 43 " pdb=" ZN G 301 " pdb="ZN ZN G 301 " - pdb=" NE2 HIS G 12 " pdb="ZN ZN G 301 " - pdb=" ND1 HIS G 16 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 43 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 40 " pdb=" ZN H 301 " pdb="ZN ZN H 301 " - pdb=" NE2 HIS H 12 " pdb="ZN ZN H 301 " - pdb=" ND1 HIS H 16 " pdb="ZN ZN H 301 " - pdb=" SG CYS H 43 " pdb="ZN ZN H 301 " - pdb=" SG CYS H 40 " pdb=" ZN I 301 " pdb="ZN ZN I 301 " - pdb=" ND1 HIS I 16 " pdb="ZN ZN I 301 " - pdb=" NE2 HIS I 12 " pdb="ZN ZN I 301 " - pdb=" SG CYS I 43 " pdb="ZN ZN I 301 " - pdb=" SG CYS I 40 " pdb=" ZN J 301 " pdb="ZN ZN J 301 " - pdb=" ND1 HIS J 16 " pdb="ZN ZN J 301 " - pdb=" NE2 HIS J 12 " pdb="ZN ZN J 301 " - pdb=" SG CYS J 40 " pdb="ZN ZN J 301 " - pdb=" SG CYS J 43 " pdb=" ZN K 301 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 40 " pdb="ZN ZN K 301 " - pdb=" NE2 HIS K 12 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 43 " pdb="ZN ZN K 301 " - pdb=" ND1 HIS K 16 " pdb=" ZN L 301 " pdb="ZN ZN L 301 " - pdb=" ND1 HIS L 16 " pdb="ZN ZN L 301 " - pdb=" NE2 HIS L 12 " pdb="ZN ZN L 301 " - pdb=" SG CYS L 43 " pdb="ZN ZN L 301 " - pdb=" SG CYS L 40 " pdb=" ZN M 301 " pdb="ZN ZN M 301 " - pdb=" ND1 HIS M 16 " pdb="ZN ZN M 301 " - pdb=" NE2 HIS M 12 " pdb="ZN ZN M 301 " - pdb=" SG CYS M 43 " pdb="ZN ZN M 301 " - pdb=" SG CYS M 40 " pdb=" ZN N 301 " pdb="ZN ZN N 301 " - pdb=" NE2 HIS N 12 " pdb="ZN ZN N 301 " - pdb=" ND1 HIS N 16 " pdb="ZN ZN N 301 " - pdb=" SG CYS N 40 " pdb="ZN ZN N 301 " - pdb=" SG CYS N 43 " pdb=" ZN O 301 " pdb="ZN ZN O 301 " - pdb=" NE2 HIS O 12 " pdb="ZN ZN O 301 " - pdb=" ND1 HIS O 16 " pdb="ZN ZN O 301 " - pdb=" SG CYS O 43 " pdb="ZN ZN O 301 " - pdb=" SG CYS O 40 " pdb=" ZN P 301 " pdb="ZN ZN P 301 " - pdb=" NE2 HIS P 12 " pdb="ZN ZN P 301 " - pdb=" ND1 HIS P 16 " pdb="ZN ZN P 301 " - pdb=" SG CYS P 43 " pdb="ZN ZN P 301 " - pdb=" SG CYS P 40 " Number of angles added : 24 10116 Ramachandran restraints generated. 5058 Oldfield, 0 Emsley, 5058 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9728 Finding SS restraints... Secondary structure from input PDB file: 233 helices and 54 sheets defined 56.4% alpha, 13.9% beta 36 base pairs and 68 stacking pairs defined. Time for finding SS restraints: 5.16 Creating SS restraints... Processing helix chain 'A' and resid 1 through 3 No H-bonds generated for 'chain 'A' and resid 1 through 3' Processing helix chain 'A' and resid 4 through 16 Processing helix chain 'A' and resid 18 through 27 Processing helix chain 'A' and resid 29 through 39 Processing helix chain 'A' and resid 40 through 46 Processing helix chain 'A' and resid 95 through 110 Processing helix chain 'A' and resid 125 through 136 Processing helix chain 'A' and resid 146 through 149 Processing helix chain 'A' and resid 150 through 168 removed outlier: 3.530A pdb=" N GLU A 154 " --> pdb=" O GLN A 150 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN A 158 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR A 159 " --> pdb=" O ARG A 155 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS A 166 " --> pdb=" O ASN A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 187 Processing helix chain 'A' and resid 196 through 214 Processing helix chain 'B' and resid 4 through 16 Processing helix chain 'B' and resid 18 through 27 Processing helix chain 'B' and resid 29 through 40 Processing helix chain 'B' and resid 40 through 46 removed outlier: 3.761A pdb=" N ASN B 46 " --> pdb=" O VAL B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 110 removed outlier: 3.695A pdb=" N MET B 104 " --> pdb=" O ARG B 100 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS B 105 " --> pdb=" O VAL B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 136 Processing helix chain 'B' and resid 146 through 168 Processing helix chain 'B' and resid 169 through 171 No H-bonds generated for 'chain 'B' and resid 169 through 171' Processing helix chain 'B' and resid 173 through 187 Processing helix chain 'B' and resid 196 through 215 removed outlier: 3.950A pdb=" N LYS B 215 " --> pdb=" O GLN B 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 16 Processing helix chain 'C' and resid 18 through 27 Processing helix chain 'C' and resid 29 through 40 removed outlier: 3.518A pdb=" N CYS C 40 " --> pdb=" O ILE C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 46 Processing helix chain 'C' and resid 95 through 106 Processing helix chain 'C' and resid 125 through 136 Processing helix chain 'C' and resid 146 through 166 removed outlier: 3.803A pdb=" N GLN C 150 " --> pdb=" O ASN C 146 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS C 166 " --> pdb=" O ASN C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 187 Processing helix chain 'C' and resid 196 through 210 removed outlier: 4.035A pdb=" N ILE C 210 " --> pdb=" O GLU C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 219 removed outlier: 4.125A pdb=" N SER C 214 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS C 217 " --> pdb=" O GLN C 213 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU C 219 " --> pdb=" O LYS C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 269 No H-bonds generated for 'chain 'C' and resid 267 through 269' Processing helix chain 'D' and resid 4 through 16 Processing helix chain 'D' and resid 18 through 27 Processing helix chain 'D' and resid 29 through 40 Processing helix chain 'D' and resid 40 through 46 removed outlier: 3.693A pdb=" N ASN D 46 " --> pdb=" O VAL D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 110 Processing helix chain 'D' and resid 125 through 136 Processing helix chain 'D' and resid 146 through 168 Processing helix chain 'D' and resid 173 through 188 removed outlier: 3.508A pdb=" N LYS D 188 " --> pdb=" O THR D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 211 removed outlier: 3.669A pdb=" N ILE D 200 " --> pdb=" O SER D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 220 Processing helix chain 'E' and resid 4 through 16 Processing helix chain 'E' and resid 18 through 27 Processing helix chain 'E' and resid 29 through 39 Processing helix chain 'E' and resid 40 through 46 removed outlier: 3.828A pdb=" N GLU E 45 " --> pdb=" O ASP E 41 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN E 46 " --> pdb=" O VAL E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 110 Processing helix chain 'E' and resid 125 through 135 Processing helix chain 'E' and resid 146 through 168 Processing helix chain 'E' and resid 173 through 187 Processing helix chain 'E' and resid 196 through 220 removed outlier: 3.529A pdb=" N GLN E 212 " --> pdb=" O GLN E 208 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN E 213 " --> pdb=" O ARG E 209 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS E 220 " --> pdb=" O SER E 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 4 through 16 removed outlier: 3.668A pdb=" N ALA F 8 " --> pdb=" O ASN F 4 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 27 Processing helix chain 'F' and resid 29 through 40 Processing helix chain 'F' and resid 40 through 46 Processing helix chain 'F' and resid 56 through 60 removed outlier: 3.647A pdb=" N GLY F 59 " --> pdb=" O ASN F 56 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ILE F 60 " --> pdb=" O LYS F 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 56 through 60' Processing helix chain 'F' and resid 95 through 110 Processing helix chain 'F' and resid 125 through 135 Processing helix chain 'F' and resid 146 through 168 Processing helix chain 'F' and resid 169 through 171 No H-bonds generated for 'chain 'F' and resid 169 through 171' Processing helix chain 'F' and resid 173 through 187 Processing helix chain 'F' and resid 196 through 215 removed outlier: 4.087A pdb=" N LYS F 215 " --> pdb=" O GLN F 211 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 16 Processing helix chain 'G' and resid 18 through 27 Processing helix chain 'G' and resid 29 through 40 Processing helix chain 'G' and resid 40 through 46 Processing helix chain 'G' and resid 95 through 109 removed outlier: 3.687A pdb=" N MET G 104 " --> pdb=" O ARG G 100 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS G 105 " --> pdb=" O VAL G 101 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N MET G 109 " --> pdb=" O LYS G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 127 through 136 removed outlier: 3.961A pdb=" N MET G 132 " --> pdb=" O THR G 128 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS G 133 " --> pdb=" O GLN G 129 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N TYR G 134 " --> pdb=" O LEU G 130 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU G 135 " --> pdb=" O LEU G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 168 removed outlier: 3.501A pdb=" N GLN G 150 " --> pdb=" O ASN G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 169 through 171 No H-bonds generated for 'chain 'G' and resid 169 through 171' Processing helix chain 'G' and resid 173 through 187 Processing helix chain 'G' and resid 196 through 211 removed outlier: 3.580A pdb=" N ILE G 210 " --> pdb=" O GLU G 206 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN G 211 " --> pdb=" O GLN G 207 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 16 Processing helix chain 'H' and resid 18 through 27 Processing helix chain 'H' and resid 29 through 40 Processing helix chain 'H' and resid 40 through 46 Processing helix chain 'H' and resid 95 through 109 removed outlier: 3.912A pdb=" N MET H 109 " --> pdb=" O LYS H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 135 Processing helix chain 'H' and resid 152 through 167 Processing helix chain 'H' and resid 173 through 187 Processing helix chain 'H' and resid 196 through 213 Processing helix chain 'a' and resid 348 through 363 Processing helix chain 'a' and resid 364 through 368 removed outlier: 3.701A pdb=" N LEU a 368 " --> pdb=" O ILE a 365 " (cutoff:3.500A) Processing helix chain 'a' and resid 369 through 382 Processing helix chain 'a' and resid 386 through 393 Processing helix chain 'a' and resid 393 through 404 Processing helix chain 'a' and resid 409 through 426 Processing helix chain 'b' and resid 348 through 363 Processing helix chain 'b' and resid 364 through 368 removed outlier: 3.796A pdb=" N LEU b 368 " --> pdb=" O ILE b 365 " (cutoff:3.500A) Processing helix chain 'b' and resid 369 through 382 Processing helix chain 'b' and resid 386 through 392 Processing helix chain 'b' and resid 393 through 404 Processing helix chain 'b' and resid 409 through 426 Processing helix chain 'c' and resid 348 through 363 Processing helix chain 'c' and resid 364 through 368 removed outlier: 4.052A pdb=" N LEU c 368 " --> pdb=" O ILE c 365 " (cutoff:3.500A) Processing helix chain 'c' and resid 369 through 382 removed outlier: 3.532A pdb=" N CYS c 373 " --> pdb=" O ASP c 369 " (cutoff:3.500A) Processing helix chain 'c' and resid 386 through 392 Processing helix chain 'c' and resid 393 through 404 Processing helix chain 'c' and resid 409 through 426 Processing helix chain 'd' and resid 348 through 363 Processing helix chain 'd' and resid 364 through 368 removed outlier: 3.568A pdb=" N LEU d 368 " --> pdb=" O ILE d 365 " (cutoff:3.500A) Processing helix chain 'd' and resid 370 through 383 Processing helix chain 'd' and resid 386 through 392 Processing helix chain 'd' and resid 393 through 404 Processing helix chain 'd' and resid 409 through 424 Processing helix chain 'e' and resid 348 through 362 Processing helix chain 'e' and resid 369 through 382 Processing helix chain 'e' and resid 386 through 392 removed outlier: 3.648A pdb=" N LYS e 392 " --> pdb=" O GLN e 388 " (cutoff:3.500A) Processing helix chain 'e' and resid 393 through 404 Processing helix chain 'e' and resid 409 through 426 Processing helix chain 'f' and resid 349 through 363 Processing helix chain 'f' and resid 364 through 368 removed outlier: 4.052A pdb=" N LEU f 368 " --> pdb=" O ILE f 365 " (cutoff:3.500A) Processing helix chain 'f' and resid 369 through 383 Processing helix chain 'f' and resid 386 through 393 Processing helix chain 'f' and resid 393 through 404 Processing helix chain 'f' and resid 409 through 426 Processing helix chain 'I' and resid 1 through 3 No H-bonds generated for 'chain 'I' and resid 1 through 3' Processing helix chain 'I' and resid 4 through 16 Processing helix chain 'I' and resid 18 through 27 Processing helix chain 'I' and resid 29 through 39 Processing helix chain 'I' and resid 40 through 46 Processing helix chain 'I' and resid 95 through 110 Processing helix chain 'I' and resid 125 through 136 Processing helix chain 'I' and resid 146 through 149 Processing helix chain 'I' and resid 150 through 168 removed outlier: 3.528A pdb=" N GLU I 154 " --> pdb=" O GLN I 150 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN I 158 " --> pdb=" O GLU I 154 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR I 159 " --> pdb=" O ARG I 155 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS I 166 " --> pdb=" O ASN I 162 " (cutoff:3.500A) Processing helix chain 'I' and resid 173 through 187 Processing helix chain 'I' and resid 196 through 214 Processing helix chain 'J' and resid 4 through 16 Processing helix chain 'J' and resid 18 through 27 Processing helix chain 'J' and resid 29 through 40 Processing helix chain 'J' and resid 40 through 46 removed outlier: 3.766A pdb=" N ASN J 46 " --> pdb=" O VAL J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 95 through 110 removed outlier: 3.683A pdb=" N MET J 104 " --> pdb=" O ARG J 100 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS J 105 " --> pdb=" O VAL J 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 125 through 136 Processing helix chain 'J' and resid 146 through 168 Processing helix chain 'J' and resid 169 through 171 No H-bonds generated for 'chain 'J' and resid 169 through 171' Processing helix chain 'J' and resid 173 through 187 Processing helix chain 'J' and resid 196 through 215 removed outlier: 3.952A pdb=" N LYS J 215 " --> pdb=" O GLN J 211 " (cutoff:3.500A) Processing helix chain 'K' and resid 4 through 16 Processing helix chain 'K' and resid 18 through 27 Processing helix chain 'K' and resid 29 through 40 removed outlier: 3.522A pdb=" N CYS K 40 " --> pdb=" O ILE K 36 " (cutoff:3.500A) Processing helix chain 'K' and resid 40 through 46 Processing helix chain 'K' and resid 95 through 106 Processing helix chain 'K' and resid 125 through 136 Processing helix chain 'K' and resid 146 through 166 removed outlier: 3.800A pdb=" N GLN K 150 " --> pdb=" O ASN K 146 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS K 166 " --> pdb=" O ASN K 162 " (cutoff:3.500A) Processing helix chain 'K' and resid 173 through 187 Processing helix chain 'K' and resid 196 through 210 removed outlier: 4.018A pdb=" N ILE K 210 " --> pdb=" O GLU K 206 " (cutoff:3.500A) Processing helix chain 'K' and resid 210 through 219 removed outlier: 4.119A pdb=" N SER K 214 " --> pdb=" O ILE K 210 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS K 217 " --> pdb=" O GLN K 213 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU K 219 " --> pdb=" O LYS K 215 " (cutoff:3.500A) Processing helix chain 'K' and resid 267 through 269 No H-bonds generated for 'chain 'K' and resid 267 through 269' Processing helix chain 'L' and resid 4 through 16 Processing helix chain 'L' and resid 18 through 27 Processing helix chain 'L' and resid 29 through 40 Processing helix chain 'L' and resid 40 through 46 removed outlier: 3.693A pdb=" N ASN L 46 " --> pdb=" O VAL L 42 " (cutoff:3.500A) Processing helix chain 'L' and resid 95 through 110 Processing helix chain 'L' and resid 125 through 136 Processing helix chain 'L' and resid 146 through 168 Processing helix chain 'L' and resid 173 through 188 removed outlier: 3.519A pdb=" N LYS L 188 " --> pdb=" O THR L 184 " (cutoff:3.500A) Processing helix chain 'L' and resid 196 through 211 Processing helix chain 'L' and resid 216 through 220 Processing helix chain 'M' and resid 4 through 16 Processing helix chain 'M' and resid 18 through 27 Processing helix chain 'M' and resid 29 through 39 Processing helix chain 'M' and resid 40 through 46 removed outlier: 3.831A pdb=" N GLU M 45 " --> pdb=" O ASP M 41 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN M 46 " --> pdb=" O VAL M 42 " (cutoff:3.500A) Processing helix chain 'M' and resid 95 through 110 Processing helix chain 'M' and resid 125 through 135 Processing helix chain 'M' and resid 146 through 168 Processing helix chain 'M' and resid 173 through 187 Processing helix chain 'M' and resid 196 through 220 removed outlier: 3.528A pdb=" N GLN M 212 " --> pdb=" O GLN M 208 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN M 213 " --> pdb=" O ARG M 209 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS M 220 " --> pdb=" O SER M 216 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 16 removed outlier: 3.658A pdb=" N ALA N 8 " --> pdb=" O ASN N 4 " (cutoff:3.500A) Processing helix chain 'N' and resid 18 through 27 Processing helix chain 'N' and resid 29 through 40 Processing helix chain 'N' and resid 40 through 46 Processing helix chain 'N' and resid 56 through 60 removed outlier: 3.639A pdb=" N GLY N 59 " --> pdb=" O ASN N 56 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ILE N 60 " --> pdb=" O LYS N 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 56 through 60' Processing helix chain 'N' and resid 95 through 110 Processing helix chain 'N' and resid 125 through 135 Processing helix chain 'N' and resid 146 through 168 Processing helix chain 'N' and resid 169 through 171 No H-bonds generated for 'chain 'N' and resid 169 through 171' Processing helix chain 'N' and resid 173 through 187 Processing helix chain 'N' and resid 196 through 215 removed outlier: 4.089A pdb=" N LYS N 215 " --> pdb=" O GLN N 211 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 16 Processing helix chain 'O' and resid 18 through 27 Processing helix chain 'O' and resid 29 through 40 Processing helix chain 'O' and resid 40 through 46 Processing helix chain 'O' and resid 95 through 109 removed outlier: 3.686A pdb=" N MET O 104 " --> pdb=" O ARG O 100 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS O 105 " --> pdb=" O VAL O 101 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N MET O 109 " --> pdb=" O LYS O 105 " (cutoff:3.500A) Processing helix chain 'O' and resid 127 through 136 removed outlier: 3.958A pdb=" N MET O 132 " --> pdb=" O THR O 128 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS O 133 " --> pdb=" O GLN O 129 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N TYR O 134 " --> pdb=" O LEU O 130 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU O 135 " --> pdb=" O LEU O 131 " (cutoff:3.500A) Processing helix chain 'O' and resid 146 through 168 Processing helix chain 'O' and resid 169 through 171 No H-bonds generated for 'chain 'O' and resid 169 through 171' Processing helix chain 'O' and resid 173 through 187 Processing helix chain 'O' and resid 196 through 211 removed outlier: 3.578A pdb=" N ILE O 210 " --> pdb=" O GLU O 206 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN O 211 " --> pdb=" O GLN O 207 " (cutoff:3.500A) Processing helix chain 'P' and resid 4 through 16 Processing helix chain 'P' and resid 18 through 27 Processing helix chain 'P' and resid 29 through 40 Processing helix chain 'P' and resid 40 through 46 Processing helix chain 'P' and resid 95 through 109 removed outlier: 3.913A pdb=" N MET P 109 " --> pdb=" O LYS P 105 " (cutoff:3.500A) Processing helix chain 'P' and resid 125 through 135 Processing helix chain 'P' and resid 152 through 167 Processing helix chain 'P' and resid 173 through 187 Processing helix chain 'P' and resid 196 through 213 Processing helix chain 'g' and resid 348 through 363 Processing helix chain 'g' and resid 364 through 368 removed outlier: 3.699A pdb=" N LEU g 368 " --> pdb=" O ILE g 365 " (cutoff:3.500A) Processing helix chain 'g' and resid 369 through 382 Processing helix chain 'g' and resid 386 through 393 Processing helix chain 'g' and resid 393 through 404 Processing helix chain 'g' and resid 409 through 426 Processing helix chain 'h' and resid 348 through 363 Processing helix chain 'h' and resid 364 through 368 removed outlier: 3.795A pdb=" N LEU h 368 " --> pdb=" O ILE h 365 " (cutoff:3.500A) Processing helix chain 'h' and resid 369 through 382 Processing helix chain 'h' and resid 386 through 392 Processing helix chain 'h' and resid 393 through 404 Processing helix chain 'h' and resid 409 through 425 Processing helix chain 'i' and resid 348 through 363 Processing helix chain 'i' and resid 364 through 368 removed outlier: 4.052A pdb=" N LEU i 368 " --> pdb=" O ILE i 365 " (cutoff:3.500A) Processing helix chain 'i' and resid 369 through 382 removed outlier: 3.529A pdb=" N CYS i 373 " --> pdb=" O ASP i 369 " (cutoff:3.500A) Processing helix chain 'i' and resid 386 through 392 Processing helix chain 'i' and resid 393 through 404 Processing helix chain 'i' and resid 409 through 426 Processing helix chain 'j' and resid 348 through 363 Processing helix chain 'j' and resid 364 through 368 removed outlier: 3.572A pdb=" N LEU j 368 " --> pdb=" O ILE j 365 " (cutoff:3.500A) Processing helix chain 'j' and resid 370 through 383 Processing helix chain 'j' and resid 386 through 392 Processing helix chain 'j' and resid 393 through 404 Processing helix chain 'j' and resid 409 through 424 Processing helix chain 'k' and resid 348 through 362 Processing helix chain 'k' and resid 364 through 368 removed outlier: 4.248A pdb=" N LEU k 368 " --> pdb=" O ILE k 365 " (cutoff:3.500A) Processing helix chain 'k' and resid 369 through 382 Processing helix chain 'k' and resid 386 through 392 removed outlier: 3.643A pdb=" N LYS k 392 " --> pdb=" O GLN k 388 " (cutoff:3.500A) Processing helix chain 'k' and resid 393 through 404 Processing helix chain 'k' and resid 409 through 426 Processing helix chain 'l' and resid 349 through 363 Processing helix chain 'l' and resid 364 through 368 removed outlier: 4.053A pdb=" N LEU l 368 " --> pdb=" O ILE l 365 " (cutoff:3.500A) Processing helix chain 'l' and resid 369 through 383 Processing helix chain 'l' and resid 386 through 393 Processing helix chain 'l' and resid 393 through 404 Processing helix chain 'l' and resid 409 through 426 Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 91 removed outlier: 4.239A pdb=" N ILE A 74 " --> pdb=" O VAL A 91 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU A 115 " --> pdb=" O THR A 140 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 260 through 265 removed outlier: 3.975A pdb=" N TRP A 245 " --> pdb=" O VAL A 252 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N LYS A 254 " --> pdb=" O VAL A 243 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N VAL A 243 " --> pdb=" O LYS A 254 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 229 through 230 Processing sheet with id=AA4, first strand: chain 'B' and resid 86 through 91 removed outlier: 4.198A pdb=" N ILE B 74 " --> pdb=" O VAL B 91 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 237 through 241 removed outlier: 4.493A pdb=" N CYS B 224 " --> pdb=" O PRO B 240 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N TYR B 225 " --> pdb=" O LYS B 270 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 250 through 255 Processing sheet with id=AA7, first strand: chain 'C' and resid 86 through 91 removed outlier: 4.269A pdb=" N ILE C 74 " --> pdb=" O VAL C 91 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TRP C 63 " --> pdb=" O SER C 114 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU C 115 " --> pdb=" O THR C 140 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 238 through 242 removed outlier: 5.215A pdb=" N GLY C 239 " --> pdb=" O TYR C 226 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N TYR C 226 " --> pdb=" O GLY C 239 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 245 through 246 removed outlier: 3.875A pdb=" N TRP C 245 " --> pdb=" O VAL C 252 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 86 through 91 removed outlier: 3.623A pdb=" N GLU D 89 " --> pdb=" O LEU D 76 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU D 76 " --> pdb=" O GLU D 89 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE D 74 " --> pdb=" O VAL D 91 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N TRP D 63 " --> pdb=" O GLN D 116 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER D 117 " --> pdb=" O THR D 140 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 238 through 242 removed outlier: 6.041A pdb=" N CYS D 224 " --> pdb=" O PRO D 240 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 245 through 246 removed outlier: 3.844A pdb=" N TRP D 245 " --> pdb=" O VAL D 252 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 86 through 91 removed outlier: 4.292A pdb=" N ILE E 74 " --> pdb=" O VAL E 91 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU E 115 " --> pdb=" O THR E 140 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 233 through 242 removed outlier: 6.472A pdb=" N GLY E 235 " --> pdb=" O LYS E 230 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LYS E 230 " --> pdb=" O GLY E 235 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N TRP E 237 " --> pdb=" O THR E 228 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N THR E 228 " --> pdb=" O TRP E 237 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N GLY E 239 " --> pdb=" O TYR E 226 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N TYR E 226 " --> pdb=" O GLY E 239 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 245 through 246 removed outlier: 3.740A pdb=" N TRP E 245 " --> pdb=" O VAL E 252 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG E 260 " --> pdb=" O ASP E 255 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 86 through 91 removed outlier: 4.128A pdb=" N ILE F 74 " --> pdb=" O VAL F 91 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TRP F 63 " --> pdb=" O SER F 114 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER F 117 " --> pdb=" O THR F 140 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 238 through 242 removed outlier: 6.242A pdb=" N CYS F 224 " --> pdb=" O PRO F 240 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 229 through 230 Processing sheet with id=AC1, first strand: chain 'F' and resid 245 through 246 removed outlier: 3.636A pdb=" N TRP F 245 " --> pdb=" O VAL F 252 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 63 through 70 removed outlier: 4.170A pdb=" N ILE G 74 " --> pdb=" O VAL G 91 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 114 through 117 Processing sheet with id=AC4, first strand: chain 'G' and resid 238 through 241 removed outlier: 6.227A pdb=" N CYS G 224 " --> pdb=" O PRO G 240 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 251 through 255 Processing sheet with id=AC6, first strand: chain 'H' and resid 86 through 91 removed outlier: 4.241A pdb=" N ILE H 74 " --> pdb=" O VAL H 91 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 241 through 242 removed outlier: 3.659A pdb=" N LYS H 270 " --> pdb=" O TYR H 225 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 229 through 230 Processing sheet with id=AC9, first strand: chain 'H' and resid 245 through 246 removed outlier: 3.699A pdb=" N TRP H 245 " --> pdb=" O VAL H 252 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 86 through 91 removed outlier: 4.242A pdb=" N ILE I 74 " --> pdb=" O VAL I 91 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU I 115 " --> pdb=" O THR I 140 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 260 through 265 removed outlier: 3.998A pdb=" N TRP I 245 " --> pdb=" O VAL I 252 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N LYS I 254 " --> pdb=" O VAL I 243 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N VAL I 243 " --> pdb=" O LYS I 254 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 229 through 230 Processing sheet with id=AD4, first strand: chain 'J' and resid 86 through 91 removed outlier: 4.196A pdb=" N ILE J 74 " --> pdb=" O VAL J 91 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 237 through 241 removed outlier: 4.503A pdb=" N CYS J 224 " --> pdb=" O PRO J 240 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N TYR J 225 " --> pdb=" O LYS J 270 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 250 through 255 Processing sheet with id=AD7, first strand: chain 'K' and resid 86 through 91 removed outlier: 4.270A pdb=" N ILE K 74 " --> pdb=" O VAL K 91 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TRP K 63 " --> pdb=" O SER K 114 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU K 115 " --> pdb=" O THR K 140 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 238 through 242 removed outlier: 5.214A pdb=" N GLY K 239 " --> pdb=" O TYR K 226 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N TYR K 226 " --> pdb=" O GLY K 239 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 245 through 246 removed outlier: 3.877A pdb=" N TRP K 245 " --> pdb=" O VAL K 252 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 86 through 91 removed outlier: 3.620A pdb=" N GLU L 89 " --> pdb=" O LEU L 76 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU L 76 " --> pdb=" O GLU L 89 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE L 74 " --> pdb=" O VAL L 91 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N TRP L 63 " --> pdb=" O GLN L 116 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER L 117 " --> pdb=" O THR L 140 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 238 through 242 removed outlier: 6.043A pdb=" N CYS L 224 " --> pdb=" O PRO L 240 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 245 through 246 removed outlier: 3.844A pdb=" N TRP L 245 " --> pdb=" O VAL L 252 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'M' and resid 86 through 91 removed outlier: 4.293A pdb=" N ILE M 74 " --> pdb=" O VAL M 91 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU M 115 " --> pdb=" O THR M 140 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'M' and resid 233 through 242 removed outlier: 6.479A pdb=" N GLY M 235 " --> pdb=" O LYS M 230 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N LYS M 230 " --> pdb=" O GLY M 235 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N TRP M 237 " --> pdb=" O THR M 228 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N THR M 228 " --> pdb=" O TRP M 237 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLY M 239 " --> pdb=" O TYR M 226 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N TYR M 226 " --> pdb=" O GLY M 239 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 245 through 246 removed outlier: 3.743A pdb=" N TRP M 245 " --> pdb=" O VAL M 252 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG M 260 " --> pdb=" O ASP M 255 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'N' and resid 86 through 91 removed outlier: 4.122A pdb=" N ILE N 74 " --> pdb=" O VAL N 91 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TRP N 63 " --> pdb=" O SER N 114 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER N 117 " --> pdb=" O THR N 140 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'N' and resid 238 through 242 removed outlier: 6.249A pdb=" N CYS N 224 " --> pdb=" O PRO N 240 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'N' and resid 229 through 230 Processing sheet with id=AF1, first strand: chain 'N' and resid 245 through 246 removed outlier: 3.627A pdb=" N TRP N 245 " --> pdb=" O VAL N 252 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'O' and resid 63 through 70 removed outlier: 4.166A pdb=" N ILE O 74 " --> pdb=" O VAL O 91 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'O' and resid 114 through 117 Processing sheet with id=AF4, first strand: chain 'O' and resid 238 through 241 removed outlier: 6.228A pdb=" N CYS O 224 " --> pdb=" O PRO O 240 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'O' and resid 245 through 246 removed outlier: 4.158A pdb=" N TRP O 245 " --> pdb=" O VAL O 252 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL O 252 " --> pdb=" O TRP O 245 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'P' and resid 86 through 91 removed outlier: 4.242A pdb=" N ILE P 74 " --> pdb=" O VAL P 91 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'P' and resid 241 through 242 removed outlier: 3.648A pdb=" N LYS P 270 " --> pdb=" O TYR P 225 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'P' and resid 229 through 230 Processing sheet with id=AF9, first strand: chain 'P' and resid 245 through 246 removed outlier: 3.705A pdb=" N TRP P 245 " --> pdb=" O VAL P 252 " (cutoff:3.500A) 2336 hydrogen bonds defined for protein. 6843 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 98 hydrogen bonds 196 hydrogen bond angles 0 basepair planarities 36 basepair parallelities 68 stacking parallelities Total time for adding SS restraints: 10.61 Time building geometry restraints manager: 4.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 11051 1.33 - 1.45: 8384 1.45 - 1.57: 24513 1.57 - 1.69: 154 1.69 - 1.81: 372 Bond restraints: 44474 Sorted by residual: bond pdb=" C3' DA Z 19 " pdb=" C2' DA Z 19 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 bond pdb=" C3' DA X 19 " pdb=" C2' DA X 19 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 bond pdb=" C3' DC W 5 " pdb=" O3' DC W 5 " ideal model delta sigma weight residual 1.435 1.401 0.034 1.30e-02 5.92e+03 6.86e+00 bond pdb=" C1' DC Y 11 " pdb=" N1 DC Y 11 " ideal model delta sigma weight residual 1.468 1.504 -0.036 1.40e-02 5.10e+03 6.74e+00 bond pdb=" C1' DC W 11 " pdb=" N1 DC W 11 " ideal model delta sigma weight residual 1.468 1.504 -0.036 1.40e-02 5.10e+03 6.72e+00 ... (remaining 44469 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.38: 59324 1.38 - 2.76: 890 2.76 - 4.14: 110 4.14 - 5.52: 33 5.52 - 6.89: 11 Bond angle restraints: 60368 Sorted by residual: angle pdb=" N3 DT Z 15 " pdb=" C4 DT Z 15 " pdb=" O4 DT Z 15 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.92e+01 angle pdb=" N3 DT X 15 " pdb=" C4 DT X 15 " pdb=" O4 DT X 15 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 angle pdb=" N3 DT W 3 " pdb=" C4 DT W 3 " pdb=" O4 DT W 3 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.80e+01 angle pdb=" N3 DT W 15 " pdb=" C4 DT W 15 " pdb=" O4 DT W 15 " ideal model delta sigma weight residual 119.90 122.43 -2.53 6.00e-01 2.78e+00 1.78e+01 angle pdb=" N3 DT Y 15 " pdb=" C4 DT Y 15 " pdb=" O4 DT Y 15 " ideal model delta sigma weight residual 119.90 122.43 -2.53 6.00e-01 2.78e+00 1.77e+01 ... (remaining 60363 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 24815 17.13 - 34.26: 1284 34.26 - 51.39: 414 51.39 - 68.52: 125 68.52 - 85.65: 20 Dihedral angle restraints: 26658 sinusoidal: 11680 harmonic: 14978 Sorted by residual: dihedral pdb=" CA PRO E 273 " pdb=" C PRO E 273 " pdb=" N PRO E 274 " pdb=" CA PRO E 274 " ideal model delta harmonic sigma weight residual -180.00 -152.24 -27.76 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" CA PRO M 273 " pdb=" C PRO M 273 " pdb=" N PRO M 274 " pdb=" CA PRO M 274 " ideal model delta harmonic sigma weight residual -180.00 -152.26 -27.74 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" CA ASN H 172 " pdb=" C ASN H 172 " pdb=" N ALA H 173 " pdb=" CA ALA H 173 " ideal model delta harmonic sigma weight residual -180.00 -157.84 -22.16 0 5.00e+00 4.00e-02 1.96e+01 ... (remaining 26655 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 4314 0.031 - 0.062: 1519 0.062 - 0.094: 472 0.094 - 0.125: 274 0.125 - 0.156: 27 Chirality restraints: 6606 Sorted by residual: chirality pdb=" CA ILE I 251 " pdb=" N ILE I 251 " pdb=" C ILE I 251 " pdb=" CB ILE I 251 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.09e-01 chirality pdb=" CA ILE A 251 " pdb=" N ILE A 251 " pdb=" C ILE A 251 " pdb=" CB ILE A 251 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.03e-01 chirality pdb=" C3' DT W 10 " pdb=" C4' DT W 10 " pdb=" O3' DT W 10 " pdb=" C2' DT W 10 " both_signs ideal model delta sigma weight residual False -2.73 -2.58 -0.15 2.00e-01 2.50e+01 5.67e-01 ... (remaining 6603 not shown) Planarity restraints: 7462 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE M 272 " 0.039 5.00e-02 4.00e+02 5.87e-02 5.52e+00 pdb=" N PRO M 273 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO M 273 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO M 273 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE E 272 " -0.039 5.00e-02 4.00e+02 5.87e-02 5.52e+00 pdb=" N PRO E 273 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO E 273 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 273 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DG W 4 " -0.030 2.00e-02 2.50e+03 1.24e-02 4.64e+00 pdb=" N9 DG W 4 " 0.029 2.00e-02 2.50e+03 pdb=" C8 DG W 4 " 0.004 2.00e-02 2.50e+03 pdb=" N7 DG W 4 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DG W 4 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DG W 4 " -0.002 2.00e-02 2.50e+03 pdb=" O6 DG W 4 " -0.010 2.00e-02 2.50e+03 pdb=" N1 DG W 4 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG W 4 " 0.002 2.00e-02 2.50e+03 pdb=" N2 DG W 4 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DG W 4 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DG W 4 " 0.003 2.00e-02 2.50e+03 ... (remaining 7459 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.00: 22360 3.00 - 3.48: 43821 3.48 - 3.95: 69225 3.95 - 4.43: 79169 4.43 - 4.90: 125455 Nonbonded interactions: 340030 Sorted by model distance: nonbonded pdb=" O5' DC Y 2 " pdb=" O4' DC Y 2 " model vdw 2.530 2.432 nonbonded pdb=" O5' DC W 2 " pdb=" O4' DC W 2 " model vdw 2.531 2.432 nonbonded pdb=" O TYR I 107 " pdb=" O PHE I 110 " model vdw 2.558 3.040 nonbonded pdb=" O TYR A 107 " pdb=" O PHE A 110 " model vdw 2.558 3.040 nonbonded pdb=" O TYR B 107 " pdb=" O PHE B 110 " model vdw 2.583 3.040 ... (remaining 340025 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: 0.05 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 or (resid 3 and (name N or name CA or name C or name O o \ r name CB )) or resid 4 through 46 or resid 60 through 145 or resid 151 through \ 213 or resid 223 through 231 or resid 234 through 265 or resid 267 through 269 o \ r (resid 270 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 01)) selection = (chain 'B' and (resid 2 or (resid 3 and (name N or name CA or name C or name O o \ r name CB )) or resid 4 through 145 or resid 151 through 213 or resid 223 throug \ h 231 or resid 234 through 265 or resid 267 through 269 or (resid 270 and (name \ N or name CA or name C or name O or name CB )) or resid 301)) selection = (chain 'C' and (resid 2 or (resid 3 and (name N or name CA or name C or name O o \ r name CB )) or resid 4 through 46 or resid 60 through 145 or resid 151 through \ 213 or resid 223 through 231 or resid 234 through 265 or resid 267 through 270 o \ r resid 301)) selection = (chain 'D' and (resid 2 or (resid 3 and (name N or name CA or name C or name O o \ r name CB )) or resid 4 through 46 or resid 60 through 145 or resid 151 through \ 213 or resid 223 through 231 or resid 234 through 265 or resid 267 through 269 o \ r (resid 270 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 01)) selection = (chain 'E' and (resid 2 or (resid 3 and (name N or name CA or name C or name O o \ r name CB )) or resid 4 through 46 or resid 60 through 145 or resid 151 through \ 213 or resid 223 through 231 or resid 234 through 265 or resid 267 through 269 o \ r (resid 270 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 01)) selection = (chain 'F' and (resid 2 through 46 or resid 60 through 145 or resid 151 through \ 213 or resid 223 through 231 or resid 234 through 265 or resid 267 through 269 o \ r (resid 270 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 01)) selection = (chain 'G' and (resid 2 or (resid 3 and (name N or name CA or name C or name O o \ r name CB )) or resid 4 through 46 or resid 60 through 145 or resid 151 through \ 269 or (resid 270 and (name N or name CA or name C or name O or name CB )) or re \ sid 301)) selection = (chain 'H' and (resid 2 or (resid 3 and (name N or name CA or name C or name O o \ r name CB )) or resid 4 through 46 or resid 60 through 213 or resid 223 through \ 231 or resid 234 through 265 or resid 267 through 269 or (resid 270 and (name N \ or name CA or name C or name O or name CB )) or resid 301)) selection = (chain 'I' and (resid 2 or (resid 3 and (name N or name CA or name C or name O o \ r name CB )) or resid 4 through 46 or resid 60 through 145 or resid 151 through \ 213 or resid 223 through 231 or resid 234 through 265 or resid 267 through 269 o \ r (resid 270 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 01)) selection = (chain 'J' and (resid 2 or (resid 3 and (name N or name CA or name C or name O o \ r name CB )) or resid 4 through 145 or resid 151 through 213 or resid 223 throug \ h 231 or resid 234 through 265 or resid 267 through 269 or (resid 270 and (name \ N or name CA or name C or name O or name CB )) or resid 301)) selection = (chain 'K' and (resid 2 or (resid 3 and (name N or name CA or name C or name O o \ r name CB )) or resid 4 through 46 or resid 60 through 145 or resid 151 through \ 213 or resid 223 through 231 or resid 234 through 265 or resid 267 through 270 o \ r resid 301)) selection = (chain 'L' and (resid 2 or (resid 3 and (name N or name CA or name C or name O o \ r name CB )) or resid 4 through 46 or resid 60 through 145 or resid 151 through \ 213 or resid 223 through 231 or resid 234 through 265 or resid 267 through 269 o \ r (resid 270 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 01)) selection = (chain 'M' and (resid 2 or (resid 3 and (name N or name CA or name C or name O o \ r name CB )) or resid 4 through 46 or resid 60 through 145 or resid 151 through \ 213 or resid 223 through 231 or resid 234 through 265 or resid 267 through 269 o \ r (resid 270 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 01)) selection = (chain 'N' and (resid 2 through 46 or resid 60 through 145 or resid 151 through \ 213 or resid 223 through 231 or resid 234 through 265 or resid 267 through 269 o \ r (resid 270 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 01)) selection = (chain 'O' and (resid 2 or (resid 3 and (name N or name CA or name C or name O o \ r name CB )) or resid 4 through 46 or resid 60 through 145 or resid 151 through \ 269 or (resid 270 and (name N or name CA or name C or name O or name CB )) or re \ sid 301)) selection = (chain 'P' and (resid 2 or (resid 3 and (name N or name CA or name C or name O o \ r name CB )) or resid 4 through 46 or resid 60 through 213 or resid 223 through \ 231 or resid 234 through 265 or resid 267 through 269 or (resid 270 and (name N \ or name CA or name C or name O or name CB )) or resid 301)) } ncs_group { reference = chain 'W' selection = chain 'Y' } ncs_group { reference = chain 'X' selection = chain 'Z' } ncs_group { reference = (chain 'a' and (resid 348 through 403 or (resid 404 through 405 and (name N or n \ ame CA or name C or name O or name CB )) or resid 406 or (resid 407 and (name N \ or name CA or name C or name O or name CB )) or resid 408 through 425)) selection = (chain 'b' and (resid 348 through 403 or (resid 404 through 405 and (name N or n \ ame CA or name C or name O or name CB )) or resid 406 through 425)) selection = (chain 'c' and (resid 348 through 403 or (resid 404 through 405 and (name N or n \ ame CA or name C or name O or name CB )) or resid 406 or (resid 407 and (name N \ or name CA or name C or name O or name CB )) or resid 408 through 425)) selection = (chain 'd' and (resid 348 through 403 or (resid 404 through 405 and (name N or n \ ame CA or name C or name O or name CB )) or resid 406 or (resid 407 and (name N \ or name CA or name C or name O or name CB )) or resid 408 through 425)) selection = (chain 'e' and (resid 348 through 403 or (resid 404 through 405 and (name N or n \ ame CA or name C or name O or name CB )) or resid 406 or (resid 407 and (name N \ or name CA or name C or name O or name CB )) or resid 408 through 425)) selection = (chain 'f' and (resid 348 through 406 or (resid 407 and (name N or name CA or na \ me C or name O or name CB )) or resid 408 through 425)) selection = (chain 'g' and (resid 348 through 403 or (resid 404 through 405 and (name N or n \ ame CA or name C or name O or name CB )) or resid 406 or (resid 407 and (name N \ or name CA or name C or name O or name CB )) or resid 408 through 425)) selection = (chain 'h' and (resid 348 through 403 or (resid 404 through 405 and (name N or n \ ame CA or name C or name O or name CB )) or resid 406 through 425)) selection = (chain 'i' and (resid 348 through 403 or (resid 404 through 405 and (name N or n \ ame CA or name C or name O or name CB )) or resid 406 or (resid 407 and (name N \ or name CA or name C or name O or name CB )) or resid 408 through 425)) selection = (chain 'j' and (resid 348 through 403 or (resid 404 through 405 and (name N or n \ ame CA or name C or name O or name CB )) or resid 406 or (resid 407 and (name N \ or name CA or name C or name O or name CB )) or resid 408 through 425)) selection = (chain 'k' and (resid 348 through 403 or (resid 404 through 405 and (name N or n \ ame CA or name C or name O or name CB )) or resid 406 or (resid 407 and (name N \ or name CA or name C or name O or name CB )) or resid 408 through 425)) selection = (chain 'l' and (resid 348 through 406 or (resid 407 and (name N or name CA or na \ me C or name O or name CB )) or resid 408 through 425)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 7.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.910 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 51.910 Find NCS groups from input model: 1.570 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: 0.000 Load rotamer database and sin/cos tables:7.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.338 44538 Z= 0.232 Angle : 0.464 11.380 60392 Z= 0.279 Chirality : 0.040 0.156 6606 Planarity : 0.003 0.059 7462 Dihedral : 12.213 85.647 16930 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.06 % Allowed : 4.62 % Favored : 94.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.12), residues: 5058 helix: 2.64 (0.10), residues: 2636 sheet: 0.77 (0.19), residues: 840 loop : -0.91 (0.15), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 53 TYR 0.010 0.001 TYR A 134 PHE 0.008 0.001 PHE M 201 TRP 0.015 0.001 TRP A 78 HIS 0.004 0.001 HIS C 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.17 (44474) covalent geometry : angle 0.43958 / 0.28 (60368) hydrogen bonds : bond 0.13487 / 9.08 ( 2434) hydrogen bonds : angle 5.22907 / 3.80 ( 7039) metal coordination : bond 0.19713 / 13.24 ( 64) metal coordination : angle 7.47043 / 5.25 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10116 Ramachandran restraints generated. 5058 Oldfield, 0 Emsley, 5058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10116 Ramachandran restraints generated. 5058 Oldfield, 0 Emsley, 5058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1249 residues out of total 4576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 1201 time to evaluate : 1.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 VAL cc_start: 0.8647 (p) cc_final: 0.8425 (t) REVERT: A 38 GLN cc_start: 0.8289 (mt0) cc_final: 0.8080 (mt0) REVERT: A 132 MET cc_start: 0.8694 (mmt) cc_final: 0.8407 (tpp) REVERT: A 241 THR cc_start: 0.7316 (t) cc_final: 0.6826 (p) REVERT: A 269 VAL cc_start: 0.8156 (t) cc_final: 0.7886 (p) REVERT: B 25 GLU cc_start: 0.7437 (tm-30) cc_final: 0.7066 (tm-30) REVERT: B 68 THR cc_start: 0.8561 (t) cc_final: 0.8324 (m) REVERT: B 124 VAL cc_start: 0.8072 (t) cc_final: 0.7774 (m) REVERT: C 268 ASP cc_start: 0.7116 (t0) cc_final: 0.6776 (t0) REVERT: E 1 TRP cc_start: 0.5316 (m-90) cc_final: 0.3487 (m-90) REVERT: E 2 ILE cc_start: 0.8467 (mm) cc_final: 0.8219 (mp) REVERT: E 11 GLU cc_start: 0.7619 (tp30) cc_final: 0.7415 (tp30) REVERT: E 61 ASP cc_start: 0.7568 (t0) cc_final: 0.7356 (t70) REVERT: E 70 TYR cc_start: 0.8002 (t80) cc_final: 0.7692 (t80) REVERT: E 113 LYS cc_start: 0.7963 (mttt) cc_final: 0.7355 (mttt) REVERT: E 132 MET cc_start: 0.6127 (tmm) cc_final: 0.5716 (tmm) REVERT: E 137 ILE cc_start: 0.7791 (mm) cc_final: 0.7091 (mm) REVERT: E 215 LYS cc_start: 0.8087 (tttt) cc_final: 0.7855 (ttpp) REVERT: E 236 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7599 (mm-30) REVERT: E 244 LEU cc_start: 0.8758 (mp) cc_final: 0.8476 (mm) REVERT: E 256 ARG cc_start: 0.7487 (mmp80) cc_final: 0.6988 (mmp80) REVERT: E 267 LYS cc_start: 0.7310 (mttt) cc_final: 0.7033 (ptpp) REVERT: E 272 ILE cc_start: 0.7461 (tt) cc_final: 0.7091 (pp) REVERT: F 56 ASN cc_start: 0.1331 (OUTLIER) cc_final: 0.0944 (t160) REVERT: F 199 ASP cc_start: 0.7234 (m-30) cc_final: 0.6994 (m-30) REVERT: G 77 VAL cc_start: 0.8200 (t) cc_final: 0.7988 (m) REVERT: G 80 GLU cc_start: 0.6897 (tm-30) cc_final: 0.6654 (tm-30) REVERT: G 116 GLN cc_start: 0.7123 (mt0) cc_final: 0.6840 (tm-30) REVERT: G 161 LYS cc_start: 0.8536 (mttt) cc_final: 0.8289 (mttt) REVERT: G 162 ASN cc_start: 0.8255 (t0) cc_final: 0.7950 (t0) REVERT: G 164 LEU cc_start: 0.7861 (tp) cc_final: 0.7626 (tm) REVERT: G 165 GLU cc_start: 0.8001 (tp30) cc_final: 0.7609 (tp30) REVERT: G 208 GLN cc_start: 0.8346 (tm-30) cc_final: 0.8010 (tm-30) REVERT: H 5 ILE cc_start: 0.8542 (mt) cc_final: 0.8297 (mm) REVERT: H 10 GLU cc_start: 0.8027 (tp30) cc_final: 0.7437 (tp30) REVERT: H 14 LYS cc_start: 0.8796 (mtmt) cc_final: 0.8176 (mtmt) REVERT: H 34 GLU cc_start: 0.8420 (mt-10) cc_final: 0.7944 (mt-10) REVERT: H 38 GLN cc_start: 0.8946 (mm-40) cc_final: 0.8680 (mm-40) REVERT: H 48 MET cc_start: 0.7050 (ppp) cc_final: 0.6802 (ppp) REVERT: H 76 LEU cc_start: 0.7628 (tp) cc_final: 0.7021 (tp) REVERT: H 85 LEU cc_start: 0.8582 (tp) cc_final: 0.8265 (tt) REVERT: H 161 LYS cc_start: 0.8731 (mtpt) cc_final: 0.8275 (mttm) REVERT: H 175 GLU cc_start: 0.6903 (mm-30) cc_final: 0.6612 (mp0) REVERT: H 200 ILE cc_start: 0.7488 (mm) cc_final: 0.7280 (mt) REVERT: H 270 LYS cc_start: 0.7087 (tptm) cc_final: 0.6411 (tptm) REVERT: a 387 MET cc_start: 0.7482 (mtm) cc_final: 0.7223 (tpp) REVERT: d 348 MET cc_start: 0.7066 (tpp) cc_final: 0.6540 (tpp) REVERT: f 396 MET cc_start: 0.7216 (ttp) cc_final: 0.6845 (ttp) REVERT: I 37 VAL cc_start: 0.8586 (p) cc_final: 0.8381 (t) REVERT: I 227 ARG cc_start: 0.8162 (ptt180) cc_final: 0.7953 (ptt180) REVERT: I 241 THR cc_start: 0.7274 (t) cc_final: 0.6827 (p) REVERT: I 259 ASP cc_start: 0.6718 (t0) cc_final: 0.6434 (t0) REVERT: I 269 VAL cc_start: 0.8345 (t) cc_final: 0.8132 (p) REVERT: I 270 LYS cc_start: 0.7855 (mtmm) cc_final: 0.7645 (mtpt) REVERT: J 25 GLU cc_start: 0.7477 (tm-30) cc_final: 0.7155 (tm-30) REVERT: J 68 THR cc_start: 0.8529 (t) cc_final: 0.8280 (m) REVERT: K 262 LEU cc_start: 0.8200 (mm) cc_final: 0.8000 (mm) REVERT: K 268 ASP cc_start: 0.7072 (t0) cc_final: 0.6867 (t0) REVERT: L 107 TYR cc_start: 0.7595 (t80) cc_final: 0.7386 (t80) REVERT: M 1 TRP cc_start: 0.5228 (m-90) cc_final: 0.3188 (m-90) REVERT: M 2 ILE cc_start: 0.8423 (mm) cc_final: 0.8180 (mp) REVERT: M 13 ASN cc_start: 0.8163 (t0) cc_final: 0.7954 (m110) REVERT: M 48 MET cc_start: 0.2860 (tpt) cc_final: 0.2003 (tpt) REVERT: M 61 ASP cc_start: 0.7675 (t0) cc_final: 0.7327 (t70) REVERT: M 70 TYR cc_start: 0.7801 (t80) cc_final: 0.7571 (t80) REVERT: M 80 GLU cc_start: 0.7522 (tm-30) cc_final: 0.7001 (tm-30) REVERT: M 107 TYR cc_start: 0.7632 (t80) cc_final: 0.7423 (t80) REVERT: M 132 MET cc_start: 0.6023 (tmm) cc_final: 0.5562 (tmm) REVERT: M 137 ILE cc_start: 0.8117 (mm) cc_final: 0.7241 (mm) REVERT: M 206 GLU cc_start: 0.8306 (tm-30) cc_final: 0.7806 (tm-30) REVERT: M 215 LYS cc_start: 0.7965 (tttt) cc_final: 0.7756 (ttpp) REVERT: M 244 LEU cc_start: 0.8723 (mp) cc_final: 0.8414 (mm) REVERT: M 255 ASP cc_start: 0.7487 (t70) cc_final: 0.6908 (t0) REVERT: M 256 ARG cc_start: 0.7421 (mmp80) cc_final: 0.7189 (mmp80) REVERT: M 276 LYS cc_start: 0.6871 (mmtt) cc_final: 0.6343 (mmtm) REVERT: N 56 ASN cc_start: 0.2993 (OUTLIER) cc_final: 0.2749 (t160) REVERT: N 69 HIS cc_start: 0.7787 (m-70) cc_final: 0.7513 (m90) REVERT: N 74 ILE cc_start: 0.7538 (mp) cc_final: 0.7252 (mm) REVERT: N 77 VAL cc_start: 0.7853 (t) cc_final: 0.7602 (m) REVERT: N 86 ILE cc_start: 0.8747 (mt) cc_final: 0.8465 (tt) REVERT: N 87 TYR cc_start: 0.8154 (t80) cc_final: 0.7953 (t80) REVERT: N 113 LYS cc_start: 0.8605 (mmmt) cc_final: 0.8258 (mmmt) REVERT: N 138 GLU cc_start: 0.7554 (tm-30) cc_final: 0.7102 (tm-30) REVERT: N 146 ASN cc_start: 0.6987 (OUTLIER) cc_final: 0.6627 (t0) REVERT: N 150 GLN cc_start: 0.8123 (mt0) cc_final: 0.7887 (mt0) REVERT: N 161 LYS cc_start: 0.8281 (mttt) cc_final: 0.7726 (mppt) REVERT: N 162 ASN cc_start: 0.7960 (m110) cc_final: 0.7392 (m110) REVERT: N 165 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7819 (mt-10) REVERT: N 187 ILE cc_start: 0.8377 (pt) cc_final: 0.8090 (tp) REVERT: N 199 ASP cc_start: 0.7661 (m-30) cc_final: 0.7262 (m-30) REVERT: N 206 GLU cc_start: 0.8340 (tp30) cc_final: 0.8111 (tp30) REVERT: N 207 GLN cc_start: 0.8697 (mm-40) cc_final: 0.8493 (mm110) REVERT: N 231 ARG cc_start: 0.8342 (mtp-110) cc_final: 0.8049 (mtp-110) REVERT: N 259 ASP cc_start: 0.7882 (t0) cc_final: 0.7504 (t0) REVERT: O 9 GLU cc_start: 0.7352 (mm-30) cc_final: 0.6979 (mm-30) REVERT: O 77 VAL cc_start: 0.8316 (t) cc_final: 0.8021 (m) REVERT: O 80 GLU cc_start: 0.6898 (tm-30) cc_final: 0.6411 (mm-30) REVERT: O 116 GLN cc_start: 0.7187 (mt0) cc_final: 0.6650 (mt0) REVERT: O 152 LEU cc_start: 0.8716 (mt) cc_final: 0.8446 (mt) REVERT: O 158 GLN cc_start: 0.8176 (mt0) cc_final: 0.7920 (mt0) REVERT: O 161 LYS cc_start: 0.8370 (mttt) cc_final: 0.8148 (mttt) REVERT: O 164 LEU cc_start: 0.8100 (tp) cc_final: 0.7735 (tm) REVERT: O 165 GLU cc_start: 0.8181 (tp30) cc_final: 0.7699 (tp30) REVERT: O 170 MET cc_start: 0.6542 (mmt) cc_final: 0.6323 (mmt) REVERT: O 208 GLN cc_start: 0.8229 (tm-30) cc_final: 0.7751 (tm-30) REVERT: P 10 GLU cc_start: 0.8313 (tp30) cc_final: 0.7747 (tp30) REVERT: P 12 HIS cc_start: 0.7071 (t70) cc_final: 0.6867 (t70) REVERT: P 14 LYS cc_start: 0.8762 (mtmt) cc_final: 0.8020 (mtmt) REVERT: P 34 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8316 (mp0) REVERT: P 42 VAL cc_start: 0.7269 (t) cc_final: 0.7038 (m) REVERT: P 48 MET cc_start: 0.3726 (ppp) cc_final: 0.3489 (ppp) REVERT: P 76 LEU cc_start: 0.7763 (tp) cc_final: 0.7208 (tm) REVERT: P 85 LEU cc_start: 0.8556 (tp) cc_final: 0.8257 (tt) REVERT: P 154 GLU cc_start: 0.7798 (tp30) cc_final: 0.7595 (tp30) REVERT: P 161 LYS cc_start: 0.8647 (mtpt) cc_final: 0.8364 (mttm) REVERT: P 165 GLU cc_start: 0.7978 (tt0) cc_final: 0.7680 (tt0) REVERT: P 175 GLU cc_start: 0.7066 (mm-30) cc_final: 0.6854 (mp0) REVERT: P 212 GLN cc_start: 0.7721 (mm-40) cc_final: 0.7484 (mm-40) REVERT: P 213 GLN cc_start: 0.6684 (pm20) cc_final: 0.6459 (pm20) REVERT: P 268 ASP cc_start: 0.7098 (m-30) cc_final: 0.6819 (t70) REVERT: h 426 MET cc_start: 0.2566 (ttm) cc_final: 0.1756 (ttt) REVERT: j 356 HIS cc_start: 0.7083 (t-170) cc_final: 0.6692 (t-90) REVERT: l 348 MET cc_start: 0.4316 (tpp) cc_final: 0.4032 (tpp) REVERT: l 426 MET cc_start: 0.0649 (ttm) cc_final: 0.0354 (ttm) outliers start: 48 outliers final: 18 residues processed: 1237 average time/residue: 0.7666 time to fit residues: 1163.3511 Evaluate side-chains 1074 residues out of total 4576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 1053 time to evaluate : 1.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 TRP Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain F residue 56 ASN Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 200 ILE Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain G residue 168 ILE Chi-restraints excluded: chain G residue 260 ARG Chi-restraints excluded: chain H residue 23 HIS Chi-restraints excluded: chain H residue 187 ILE Chi-restraints excluded: chain I residue 1 TRP Chi-restraints excluded: chain I residue 119 ASN Chi-restraints excluded: chain L residue 253 VAL Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain N residue 56 ASN Chi-restraints excluded: chain N residue 146 ASN Chi-restraints excluded: chain N residue 244 LEU Chi-restraints excluded: chain N residue 251 ILE Chi-restraints excluded: chain O residue 260 ARG Chi-restraints excluded: chain P residue 23 HIS Chi-restraints excluded: chain P residue 187 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 432 optimal weight: 0.0060 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 0.7980 chunk 455 optimal weight: 0.0970 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 494 optimal weight: 0.4980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 50.0000 chunk 207 optimal weight: 6.9990 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 97 GLN A 148 GLN A 238 GLN A 266 ASN B 17 GLN ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 17 GLN E 119 ASN E 211 GLN E 242 GLN ** F 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 HIS F 82 ASN ** F 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 204 ASN F 208 GLN F 266 ASN ** G 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 13 ASN H 69 HIS I 97 GLN I 213 GLN J 17 GLN J 116 GLN J 129 GLN ** K 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 162 ASN M 119 ASN M 211 GLN M 242 GLN N 17 GLN ** N 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 82 ASN ** N 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 172 ASN N 208 GLN N 266 ASN O 64 GLN O 162 ASN O 204 ASN ** P 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 158 GLN P 207 GLN k 361 ASN k 367 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.211020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.160674 restraints weight = 66032.927| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 2.87 r_work: 0.3718 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.184 44538 Z= 0.135 Angle : 0.552 10.609 60392 Z= 0.293 Chirality : 0.042 0.266 6606 Planarity : 0.004 0.060 7462 Dihedral : 13.049 74.949 6382 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.41 % Allowed : 13.40 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.12), residues: 5058 helix: 2.59 (0.10), residues: 2668 sheet: 0.65 (0.18), residues: 896 loop : -0.95 (0.15), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG N 90 TYR 0.037 0.001 TYR L 70 PHE 0.018 0.001 PHE C 26 TRP 0.018 0.001 TRP I 106 HIS 0.016 0.002 HIS F 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (44474) covalent geometry : angle 0.54451 / 0.29 (60368) hydrogen bonds : bond 0.04288 / 2.91 ( 2434) hydrogen bonds : angle 4.20431 / 3.05 ( 7039) metal coordination : bond 0.04502 / 2.96 ( 64) metal coordination : angle 4.56435 / 3.78 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10116 Ramachandran restraints generated. 5058 Oldfield, 0 Emsley, 5058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10116 Ramachandran restraints generated. 5058 Oldfield, 0 Emsley, 5058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1223 residues out of total 4576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 1068 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7509 (tt0) REVERT: A 241 THR cc_start: 0.7897 (t) cc_final: 0.7643 (p) REVERT: B 25 GLU cc_start: 0.7235 (tm-30) cc_final: 0.6883 (tm-30) REVERT: B 68 THR cc_start: 0.8595 (t) cc_final: 0.8261 (m) REVERT: B 124 VAL cc_start: 0.8091 (t) cc_final: 0.7824 (m) REVERT: C 25 GLU cc_start: 0.7526 (tm-30) cc_final: 0.6837 (tm-30) REVERT: C 37 VAL cc_start: 0.8496 (t) cc_final: 0.8200 (t) REVERT: C 76 LEU cc_start: 0.6946 (mt) cc_final: 0.6746 (mm) REVERT: C 268 ASP cc_start: 0.7127 (t0) cc_final: 0.6557 (t0) REVERT: D 109 MET cc_start: 0.6773 (mmm) cc_final: 0.6454 (tpp) REVERT: D 132 MET cc_start: 0.5937 (ppp) cc_final: 0.5693 (ppp) REVERT: D 188 LYS cc_start: 0.7249 (mmtt) cc_final: 0.6753 (mmtt) REVERT: D 207 GLN cc_start: 0.7232 (OUTLIER) cc_final: 0.6880 (mp10) REVERT: E 1 TRP cc_start: 0.4956 (m-90) cc_final: 0.2971 (m-90) REVERT: E 34 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7524 (mm-30) REVERT: E 70 TYR cc_start: 0.8179 (t80) cc_final: 0.7871 (t80) REVERT: E 80 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.6687 (tm-30) REVERT: E 113 LYS cc_start: 0.7822 (mttt) cc_final: 0.7411 (mttt) REVERT: E 132 MET cc_start: 0.6008 (tmm) cc_final: 0.5762 (tmm) REVERT: E 137 ILE cc_start: 0.8194 (mm) cc_final: 0.7589 (mm) REVERT: E 208 GLN cc_start: 0.8383 (tt0) cc_final: 0.7911 (tt0) REVERT: F 56 ASN cc_start: 0.2085 (OUTLIER) cc_final: 0.1840 (t160) REVERT: F 87 TYR cc_start: 0.8372 (t80) cc_final: 0.8148 (t80) REVERT: F 150 GLN cc_start: 0.7633 (mt0) cc_final: 0.7308 (mt0) REVERT: F 168 ILE cc_start: 0.8665 (OUTLIER) cc_final: 0.8356 (OUTLIER) REVERT: F 199 ASP cc_start: 0.7569 (m-30) cc_final: 0.7227 (m-30) REVERT: F 206 GLU cc_start: 0.8041 (tp30) cc_final: 0.7497 (tp30) REVERT: F 209 ARG cc_start: 0.8415 (OUTLIER) cc_final: 0.7285 (tmm160) REVERT: G 24 LEU cc_start: 0.8857 (mt) cc_final: 0.8585 (mp) REVERT: G 82 ASN cc_start: 0.7406 (m-40) cc_final: 0.7204 (m-40) REVERT: G 164 LEU cc_start: 0.7859 (tp) cc_final: 0.7646 (tm) REVERT: G 165 GLU cc_start: 0.8065 (tp30) cc_final: 0.7644 (tp30) REVERT: G 208 GLN cc_start: 0.8115 (tm-30) cc_final: 0.7864 (tm-30) REVERT: H 10 GLU cc_start: 0.7447 (tp30) cc_final: 0.6478 (tp30) REVERT: H 14 LYS cc_start: 0.8758 (mtmt) cc_final: 0.7979 (mtmt) REVERT: H 34 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7412 (mt-10) REVERT: H 38 GLN cc_start: 0.8602 (mm-40) cc_final: 0.8367 (mm-40) REVERT: H 48 MET cc_start: 0.7061 (ppp) cc_final: 0.6844 (ppp) REVERT: H 76 LEU cc_start: 0.7854 (tp) cc_final: 0.7439 (tp) REVERT: H 102 GLN cc_start: 0.7968 (mm-40) cc_final: 0.7407 (mm-40) REVERT: H 254 LYS cc_start: 0.7390 (ttmt) cc_final: 0.7109 (ttmm) REVERT: a 387 MET cc_start: 0.7014 (mtm) cc_final: 0.6698 (tpp) REVERT: a 413 MET cc_start: 0.6423 (mtp) cc_final: 0.6180 (mtp) REVERT: b 348 MET cc_start: 0.4365 (OUTLIER) cc_final: 0.2788 (ttm) REVERT: b 426 MET cc_start: 0.4194 (ttm) cc_final: 0.3544 (ttt) REVERT: d 348 MET cc_start: 0.7008 (tpp) cc_final: 0.6517 (tpp) REVERT: f 396 MET cc_start: 0.8492 (ttp) cc_final: 0.8076 (ttp) REVERT: I 241 THR cc_start: 0.7904 (t) cc_final: 0.7616 (p) REVERT: I 259 ASP cc_start: 0.7083 (t0) cc_final: 0.6865 (t0) REVERT: J 25 GLU cc_start: 0.7365 (tm-30) cc_final: 0.7043 (tm-30) REVERT: J 68 THR cc_start: 0.8575 (t) cc_final: 0.8300 (m) REVERT: J 124 VAL cc_start: 0.7954 (t) cc_final: 0.7608 (m) REVERT: K 25 GLU cc_start: 0.7605 (tm-30) cc_final: 0.6924 (tm-30) REVERT: K 262 LEU cc_start: 0.7942 (mm) cc_final: 0.7636 (mm) REVERT: K 268 ASP cc_start: 0.7260 (t0) cc_final: 0.6794 (t0) REVERT: L 132 MET cc_start: 0.6182 (ppp) cc_final: 0.5678 (ppp) REVERT: L 188 LYS cc_start: 0.7093 (mmtt) cc_final: 0.6701 (mmtt) REVERT: L 207 GLN cc_start: 0.7148 (OUTLIER) cc_final: 0.6677 (mp10) REVERT: M 1 TRP cc_start: 0.4832 (m-90) cc_final: 0.2679 (m-90) REVERT: M 13 ASN cc_start: 0.8168 (t0) cc_final: 0.7967 (t0) REVERT: M 34 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7558 (mm-30) REVERT: M 48 MET cc_start: 0.2661 (tpt) cc_final: 0.1856 (tpt) REVERT: M 61 ASP cc_start: 0.7544 (t0) cc_final: 0.7320 (t70) REVERT: M 80 GLU cc_start: 0.7352 (tm-30) cc_final: 0.7043 (tm-30) REVERT: M 107 TYR cc_start: 0.7685 (t80) cc_final: 0.7427 (t80) REVERT: M 255 ASP cc_start: 0.7775 (t70) cc_final: 0.7361 (t0) REVERT: N 113 LYS cc_start: 0.8533 (mmmt) cc_final: 0.8304 (mmmt) REVERT: N 146 ASN cc_start: 0.6425 (OUTLIER) cc_final: 0.6218 (t0) REVERT: N 157 HIS cc_start: 0.8336 (m170) cc_final: 0.7852 (m90) REVERT: N 161 LYS cc_start: 0.8237 (mttt) cc_final: 0.7824 (mppt) REVERT: N 162 ASN cc_start: 0.7946 (m110) cc_final: 0.7534 (m110) REVERT: N 199 ASP cc_start: 0.7649 (m-30) cc_final: 0.7335 (m-30) REVERT: N 231 ARG cc_start: 0.7765 (mtp-110) cc_final: 0.7512 (mtp-110) REVERT: N 251 ILE cc_start: 0.8267 (OUTLIER) cc_final: 0.8048 (pt) REVERT: O 80 GLU cc_start: 0.7133 (tm-30) cc_final: 0.6723 (mm-30) REVERT: O 116 GLN cc_start: 0.7017 (mt0) cc_final: 0.6730 (mt0) REVERT: O 152 LEU cc_start: 0.8690 (mt) cc_final: 0.8422 (mt) REVERT: O 161 LYS cc_start: 0.8596 (mttt) cc_final: 0.8386 (mttt) REVERT: O 164 LEU cc_start: 0.8130 (tp) cc_final: 0.7760 (tm) REVERT: O 165 GLU cc_start: 0.8207 (tp30) cc_final: 0.7686 (tp30) REVERT: O 170 MET cc_start: 0.6677 (mmt) cc_final: 0.6386 (mmt) REVERT: O 208 GLN cc_start: 0.8136 (tm-30) cc_final: 0.7720 (tm-30) REVERT: P 10 GLU cc_start: 0.7511 (tp30) cc_final: 0.7136 (tp30) REVERT: P 14 LYS cc_start: 0.8680 (mtmt) cc_final: 0.7695 (mtmt) REVERT: P 48 MET cc_start: 0.4338 (ppp) cc_final: 0.3929 (ppp) REVERT: P 76 LEU cc_start: 0.7933 (tp) cc_final: 0.7584 (tm) REVERT: P 85 LEU cc_start: 0.8808 (tp) cc_final: 0.8603 (tt) REVERT: P 165 GLU cc_start: 0.7425 (tt0) cc_final: 0.7220 (tt0) REVERT: P 221 ILE cc_start: 0.8094 (mp) cc_final: 0.7889 (mm) REVERT: P 223 PHE cc_start: 0.8807 (m-80) cc_final: 0.8539 (m-80) REVERT: P 254 LYS cc_start: 0.7382 (ttmm) cc_final: 0.7125 (tptm) REVERT: P 268 ASP cc_start: 0.7195 (m-30) cc_final: 0.6914 (t70) REVERT: h 426 MET cc_start: 0.3450 (ttm) cc_final: 0.2560 (ttt) REVERT: j 356 HIS cc_start: 0.7146 (t-170) cc_final: 0.6905 (t-170) REVERT: l 348 MET cc_start: 0.4427 (tpp) cc_final: 0.4086 (tpp) REVERT: l 387 MET cc_start: 0.6596 (mtm) cc_final: 0.6319 (mtm) REVERT: l 426 MET cc_start: 0.2194 (ttm) cc_final: 0.1874 (ttm) outliers start: 155 outliers final: 61 residues processed: 1128 average time/residue: 0.7505 time to fit residues: 1026.9477 Evaluate side-chains 1098 residues out of total 4576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 1028 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 TRP Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 190 LYS Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 207 GLN Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 80 GLU Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain F residue 16 HIS Chi-restraints excluded: chain F residue 56 ASN Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 209 ARG Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 204 ASN Chi-restraints excluded: chain G residue 260 ARG Chi-restraints excluded: chain H residue 23 HIS Chi-restraints excluded: chain H residue 104 MET Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain H residue 264 ILE Chi-restraints excluded: chain b residue 348 MET Chi-restraints excluded: chain d residue 403 ILE Chi-restraints excluded: chain I residue 1 TRP Chi-restraints excluded: chain I residue 168 ILE Chi-restraints excluded: chain I residue 210 ILE Chi-restraints excluded: chain I residue 253 VAL Chi-restraints excluded: chain J residue 17 GLN Chi-restraints excluded: chain J residue 138 GLU Chi-restraints excluded: chain J residue 168 ILE Chi-restraints excluded: chain K residue 104 MET Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 241 THR Chi-restraints excluded: chain L residue 113 LYS Chi-restraints excluded: chain L residue 128 THR Chi-restraints excluded: chain L residue 207 GLN Chi-restraints excluded: chain L residue 253 VAL Chi-restraints excluded: chain L residue 264 ILE Chi-restraints excluded: chain M residue 10 GLU Chi-restraints excluded: chain M residue 210 ILE Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain N residue 16 HIS Chi-restraints excluded: chain N residue 76 LEU Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 114 SER Chi-restraints excluded: chain N residue 133 LYS Chi-restraints excluded: chain N residue 143 ILE Chi-restraints excluded: chain N residue 146 ASN Chi-restraints excluded: chain N residue 166 LYS Chi-restraints excluded: chain N residue 195 THR Chi-restraints excluded: chain N residue 244 LEU Chi-restraints excluded: chain N residue 251 ILE Chi-restraints excluded: chain O residue 67 TYR Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 260 ARG Chi-restraints excluded: chain P residue 18 ASP Chi-restraints excluded: chain P residue 23 HIS Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain P residue 162 ASN Chi-restraints excluded: chain P residue 263 VAL Chi-restraints excluded: chain j residue 359 ILE Chi-restraints excluded: chain k residue 426 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 24 optimal weight: 0.5980 chunk 342 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 390 optimal weight: 1.9990 chunk 383 optimal weight: 0.7980 chunk 271 optimal weight: 0.7980 chunk 75 optimal weight: 4.9990 chunk 328 optimal weight: 1.9990 chunk 474 optimal weight: 9.9990 chunk 167 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 97 GLN A 148 GLN A 150 GLN ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 ASN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 17 GLN E 139 HIS E 242 GLN ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 HIS ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 HIS F 82 ASN ** F 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 116 GLN G 186 ASN ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 393 HIS I 150 GLN I 266 ASN J 116 GLN J 129 GLN ** K 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 38 GLN M 139 HIS M 213 GLN M 242 GLN ** N 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 17 GLN N 23 HIS ** N 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 69 HIS N 82 ASN ** N 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 266 ASN O 64 GLN ** O 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 139 HIS O 162 ASN O 186 ASN O 204 ASN ** P 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 207 GLN i 393 HIS Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.208818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.157840 restraints weight = 65451.710| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 2.77 r_work: 0.3699 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.200 44538 Z= 0.157 Angle : 0.556 12.631 60392 Z= 0.293 Chirality : 0.042 0.316 6606 Planarity : 0.004 0.059 7462 Dihedral : 13.096 75.378 6368 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.69 % Favored : 97.29 % Rotamer: Outliers : 3.85 % Allowed : 15.53 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.12), residues: 5058 helix: 2.49 (0.10), residues: 2682 sheet: 0.60 (0.17), residues: 890 loop : -1.06 (0.15), residues: 1486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.000 ARG F 90 TYR 0.019 0.001 TYR O 225 PHE 0.019 0.001 PHE h 406 TRP 0.018 0.001 TRP I 106 HIS 0.018 0.002 HIS F 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (44474) covalent geometry : angle 0.54501 / 0.29 (60368) hydrogen bonds : bond 0.04213 / 2.85 ( 2434) hydrogen bonds : angle 4.09185 / 2.97 ( 7039) metal coordination : bond 0.04413 / 2.96 ( 64) metal coordination : angle 5.56921 / 4.50 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10116 Ramachandran restraints generated. 5058 Oldfield, 0 Emsley, 5058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10116 Ramachandran restraints generated. 5058 Oldfield, 0 Emsley, 5058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1213 residues out of total 4576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 1038 time to evaluate : 1.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7454 (tt0) REVERT: A 227 ARG cc_start: 0.8136 (ptt180) cc_final: 0.7486 (ptm-80) REVERT: A 241 THR cc_start: 0.7897 (t) cc_final: 0.7640 (p) REVERT: B 25 GLU cc_start: 0.7212 (tm-30) cc_final: 0.6853 (tm-30) REVERT: B 68 THR cc_start: 0.8500 (t) cc_final: 0.8212 (m) REVERT: B 124 VAL cc_start: 0.8162 (t) cc_final: 0.7953 (m) REVERT: B 262 LEU cc_start: 0.6925 (OUTLIER) cc_final: 0.6519 (mm) REVERT: C 9 GLU cc_start: 0.8092 (tt0) cc_final: 0.7882 (tt0) REVERT: C 13 ASN cc_start: 0.8651 (OUTLIER) cc_final: 0.8376 (m-40) REVERT: C 24 LEU cc_start: 0.8491 (mm) cc_final: 0.8264 (mp) REVERT: C 25 GLU cc_start: 0.7523 (tm-30) cc_final: 0.6888 (tm-30) REVERT: C 76 LEU cc_start: 0.7203 (mt) cc_final: 0.6992 (mm) REVERT: C 268 ASP cc_start: 0.7038 (t0) cc_final: 0.6523 (t0) REVERT: D 109 MET cc_start: 0.6814 (mmm) cc_final: 0.6524 (tpp) REVERT: D 132 MET cc_start: 0.5820 (ppp) cc_final: 0.5465 (ppp) REVERT: D 188 LYS cc_start: 0.7361 (mmtt) cc_final: 0.6750 (mmtt) REVERT: D 207 GLN cc_start: 0.7151 (OUTLIER) cc_final: 0.6790 (mp10) REVERT: E 1 TRP cc_start: 0.4824 (m-90) cc_final: 0.2838 (m-90) REVERT: E 34 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7688 (mm-30) REVERT: E 137 ILE cc_start: 0.8217 (mm) cc_final: 0.7618 (mm) REVERT: E 207 GLN cc_start: 0.8471 (tp40) cc_final: 0.8219 (mm-40) REVERT: E 255 ASP cc_start: 0.7907 (t0) cc_final: 0.7356 (t0) REVERT: F 56 ASN cc_start: 0.2141 (OUTLIER) cc_final: 0.1908 (t160) REVERT: F 150 GLN cc_start: 0.7702 (mt0) cc_final: 0.7390 (mt0) REVERT: F 199 ASP cc_start: 0.7593 (m-30) cc_final: 0.7258 (m-30) REVERT: F 206 GLU cc_start: 0.8027 (tp30) cc_final: 0.7473 (tp30) REVERT: F 209 ARG cc_start: 0.8399 (OUTLIER) cc_final: 0.7282 (tmm160) REVERT: G 80 GLU cc_start: 0.7188 (tm-30) cc_final: 0.6480 (tm-30) REVERT: G 161 LYS cc_start: 0.8696 (mttt) cc_final: 0.8445 (mttt) REVERT: G 164 LEU cc_start: 0.7909 (tp) cc_final: 0.7638 (tm) REVERT: G 165 GLU cc_start: 0.8049 (tp30) cc_final: 0.7601 (tp30) REVERT: G 208 GLN cc_start: 0.8183 (tm-30) cc_final: 0.7939 (tm-30) REVERT: H 10 GLU cc_start: 0.7277 (tp30) cc_final: 0.6878 (tp30) REVERT: H 14 LYS cc_start: 0.8754 (mtmt) cc_final: 0.7979 (mtmt) REVERT: H 17 GLN cc_start: 0.8124 (pm20) cc_final: 0.7890 (pm20) REVERT: H 34 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7552 (mt-10) REVERT: H 38 GLN cc_start: 0.8692 (mm-40) cc_final: 0.8432 (mm-40) REVERT: H 48 MET cc_start: 0.7061 (ppp) cc_final: 0.6860 (ppp) REVERT: H 76 LEU cc_start: 0.7849 (tp) cc_final: 0.7583 (tm) REVERT: H 254 LYS cc_start: 0.7467 (OUTLIER) cc_final: 0.7206 (ttmm) REVERT: a 387 MET cc_start: 0.7117 (mtm) cc_final: 0.6843 (tpp) REVERT: a 413 MET cc_start: 0.6315 (mtp) cc_final: 0.6057 (mtp) REVERT: b 426 MET cc_start: 0.4040 (ttm) cc_final: 0.3476 (ttp) REVERT: d 348 MET cc_start: 0.6976 (tpp) cc_final: 0.6479 (tpp) REVERT: d 413 MET cc_start: 0.7154 (mmt) cc_final: 0.6949 (mmt) REVERT: e 413 MET cc_start: 0.6138 (mtp) cc_final: 0.5878 (mtp) REVERT: f 396 MET cc_start: 0.8471 (ttp) cc_final: 0.8012 (ttp) REVERT: I 241 THR cc_start: 0.7907 (t) cc_final: 0.7648 (p) REVERT: I 259 ASP cc_start: 0.7098 (t0) cc_final: 0.6866 (t0) REVERT: J 20 VAL cc_start: 0.6958 (m) cc_final: 0.6733 (p) REVERT: J 25 GLU cc_start: 0.7219 (tm-30) cc_final: 0.6874 (tm-30) REVERT: J 68 THR cc_start: 0.8517 (t) cc_final: 0.8236 (m) REVERT: J 124 VAL cc_start: 0.8027 (t) cc_final: 0.7741 (m) REVERT: J 132 MET cc_start: 0.8813 (tpp) cc_final: 0.8602 (mmt) REVERT: J 207 GLN cc_start: 0.8066 (OUTLIER) cc_final: 0.7487 (mp10) REVERT: J 262 LEU cc_start: 0.7315 (OUTLIER) cc_final: 0.7034 (mm) REVERT: K 166 LYS cc_start: 0.8677 (pttt) cc_final: 0.8434 (pttt) REVERT: K 254 LYS cc_start: 0.7956 (tttp) cc_final: 0.7592 (tptm) REVERT: K 262 LEU cc_start: 0.7905 (mm) cc_final: 0.7598 (mm) REVERT: K 268 ASP cc_start: 0.7284 (t0) cc_final: 0.6814 (t0) REVERT: L 132 MET cc_start: 0.6033 (ppp) cc_final: 0.5645 (ppp) REVERT: L 188 LYS cc_start: 0.7166 (mmtt) cc_final: 0.6756 (mmtt) REVERT: L 207 GLN cc_start: 0.7051 (OUTLIER) cc_final: 0.6573 (mp10) REVERT: M 1 TRP cc_start: 0.4902 (m-90) cc_final: 0.2748 (m-90) REVERT: M 34 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7587 (mm-30) REVERT: M 48 MET cc_start: 0.2679 (tpt) cc_final: 0.1828 (tpt) REVERT: M 61 ASP cc_start: 0.7522 (t0) cc_final: 0.7268 (t70) REVERT: M 80 GLU cc_start: 0.7343 (tm-30) cc_final: 0.7069 (tm-30) REVERT: M 107 TYR cc_start: 0.7820 (t80) cc_final: 0.7523 (t80) REVERT: N 113 LYS cc_start: 0.8518 (mmmt) cc_final: 0.8299 (mmmt) REVERT: N 146 ASN cc_start: 0.6093 (OUTLIER) cc_final: 0.5763 (t0) REVERT: N 150 GLN cc_start: 0.7665 (mt0) cc_final: 0.7408 (mt0) REVERT: N 162 ASN cc_start: 0.7989 (m110) cc_final: 0.7584 (m110) REVERT: N 199 ASP cc_start: 0.7611 (m-30) cc_final: 0.7283 (m-30) REVERT: N 231 ARG cc_start: 0.7783 (mtp-110) cc_final: 0.7537 (mtp-110) REVERT: N 251 ILE cc_start: 0.8209 (OUTLIER) cc_final: 0.7987 (pt) REVERT: O 9 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7314 (mm-30) REVERT: O 80 GLU cc_start: 0.7164 (tm-30) cc_final: 0.6741 (mm-30) REVERT: O 116 GLN cc_start: 0.6923 (mt0) cc_final: 0.6691 (mt0) REVERT: O 152 LEU cc_start: 0.8619 (mt) cc_final: 0.8357 (mt) REVERT: O 161 LYS cc_start: 0.8605 (mttt) cc_final: 0.8380 (mttt) REVERT: O 164 LEU cc_start: 0.8221 (tp) cc_final: 0.7901 (tm) REVERT: O 165 GLU cc_start: 0.8247 (tp30) cc_final: 0.7723 (tp30) REVERT: O 170 MET cc_start: 0.6725 (mmt) cc_final: 0.6450 (mmt) REVERT: O 208 GLN cc_start: 0.8152 (tm-30) cc_final: 0.7741 (tm-30) REVERT: O 212 GLN cc_start: 0.6554 (OUTLIER) cc_final: 0.6295 (mp-120) REVERT: P 10 GLU cc_start: 0.7627 (tp30) cc_final: 0.7223 (tp30) REVERT: P 14 LYS cc_start: 0.8729 (mtmt) cc_final: 0.7749 (mtmt) REVERT: P 48 MET cc_start: 0.4338 (ppp) cc_final: 0.3941 (ppp) REVERT: P 76 LEU cc_start: 0.7954 (tp) cc_final: 0.7652 (tm) REVERT: P 85 LEU cc_start: 0.8738 (tp) cc_final: 0.8502 (tt) REVERT: P 254 LYS cc_start: 0.7513 (ttmm) cc_final: 0.7273 (tptm) REVERT: P 276 LYS cc_start: 0.5688 (OUTLIER) cc_final: 0.4307 (mtmt) REVERT: h 426 MET cc_start: 0.3379 (ttm) cc_final: 0.2448 (ttt) REVERT: k 387 MET cc_start: 0.7896 (mmm) cc_final: 0.7368 (tpt) REVERT: l 348 MET cc_start: 0.4397 (tpp) cc_final: 0.4088 (tpp) REVERT: l 387 MET cc_start: 0.6594 (mtm) cc_final: 0.6333 (mtm) REVERT: l 426 MET cc_start: 0.2177 (ttm) cc_final: 0.1857 (ttm) outliers start: 175 outliers final: 90 residues processed: 1101 average time/residue: 0.8078 time to fit residues: 1075.9875 Evaluate side-chains 1102 residues out of total 4576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 998 time to evaluate : 1.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 TRP Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 190 LYS Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain C residue 3 GLU Chi-restraints excluded: chain C residue 13 ASN Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain D residue 207 GLN Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain F residue 16 HIS Chi-restraints excluded: chain F residue 56 ASN Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 195 THR Chi-restraints excluded: chain F residue 209 ARG Chi-restraints excluded: chain G residue 11 GLU Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 260 ARG Chi-restraints excluded: chain H residue 23 HIS Chi-restraints excluded: chain H residue 104 MET Chi-restraints excluded: chain H residue 198 MET Chi-restraints excluded: chain H residue 254 LYS Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain b residue 419 LEU Chi-restraints excluded: chain c residue 378 ASP Chi-restraints excluded: chain d residue 403 ILE Chi-restraints excluded: chain I residue 1 TRP Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 119 ASN Chi-restraints excluded: chain I residue 133 LYS Chi-restraints excluded: chain I residue 168 ILE Chi-restraints excluded: chain I residue 227 ARG Chi-restraints excluded: chain I residue 251 ILE Chi-restraints excluded: chain I residue 253 VAL Chi-restraints excluded: chain J residue 92 LYS Chi-restraints excluded: chain J residue 133 LYS Chi-restraints excluded: chain J residue 137 ILE Chi-restraints excluded: chain J residue 138 GLU Chi-restraints excluded: chain J residue 168 ILE Chi-restraints excluded: chain J residue 193 LEU Chi-restraints excluded: chain J residue 207 GLN Chi-restraints excluded: chain J residue 262 LEU Chi-restraints excluded: chain K residue 104 MET Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 205 LYS Chi-restraints excluded: chain K residue 241 THR Chi-restraints excluded: chain L residue 127 SER Chi-restraints excluded: chain L residue 128 THR Chi-restraints excluded: chain L residue 207 GLN Chi-restraints excluded: chain L residue 253 VAL Chi-restraints excluded: chain L residue 264 ILE Chi-restraints excluded: chain M residue 10 GLU Chi-restraints excluded: chain M residue 17 GLN Chi-restraints excluded: chain M residue 207 GLN Chi-restraints excluded: chain M residue 210 ILE Chi-restraints excluded: chain M residue 244 LEU Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 264 ILE Chi-restraints excluded: chain N residue 16 HIS Chi-restraints excluded: chain N residue 133 LYS Chi-restraints excluded: chain N residue 143 ILE Chi-restraints excluded: chain N residue 146 ASN Chi-restraints excluded: chain N residue 155 ARG Chi-restraints excluded: chain N residue 166 LYS Chi-restraints excluded: chain N residue 168 ILE Chi-restraints excluded: chain N residue 195 THR Chi-restraints excluded: chain N residue 244 LEU Chi-restraints excluded: chain N residue 251 ILE Chi-restraints excluded: chain O residue 67 TYR Chi-restraints excluded: chain O residue 187 ILE Chi-restraints excluded: chain O residue 212 GLN Chi-restraints excluded: chain O residue 260 ARG Chi-restraints excluded: chain O residue 264 ILE Chi-restraints excluded: chain P residue 18 ASP Chi-restraints excluded: chain P residue 23 HIS Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain P residue 162 ASN Chi-restraints excluded: chain P residue 164 LEU Chi-restraints excluded: chain P residue 252 VAL Chi-restraints excluded: chain P residue 263 VAL Chi-restraints excluded: chain P residue 276 LYS Chi-restraints excluded: chain g residue 396 MET Chi-restraints excluded: chain h residue 387 MET Chi-restraints excluded: chain i residue 426 MET Chi-restraints excluded: chain k residue 426 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 421 optimal weight: 0.0670 chunk 283 optimal weight: 7.9990 chunk 75 optimal weight: 0.9990 chunk 209 optimal weight: 7.9990 chunk 368 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 500 optimal weight: 0.9980 chunk 364 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 418 optimal weight: 2.9990 overall best weight: 0.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 GLN ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 GLN E 139 HIS E 208 GLN E 211 GLN E 242 GLN ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 17 GLN ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 HIS F 82 ASN ** F 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 172 ASN F 266 ASN ** G 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 116 GLN J 129 GLN ** K 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 44 GLN ** L 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 139 HIS M 212 GLN M 242 GLN ** N 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 69 HIS N 82 ASN ** N 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 172 ASN N 266 ASN ** O 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 82 ASN O 162 ASN ** P 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.207615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.157039 restraints weight = 65389.387| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 2.91 r_work: 0.3644 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.183 44538 Z= 0.173 Angle : 0.577 16.994 60392 Z= 0.301 Chirality : 0.043 0.214 6606 Planarity : 0.004 0.061 7462 Dihedral : 13.139 75.528 6368 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.60 % Allowed : 15.40 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.12), residues: 5058 helix: 2.42 (0.10), residues: 2682 sheet: 0.55 (0.18), residues: 870 loop : -1.19 (0.15), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 155 TYR 0.021 0.002 TYR O 70 PHE 0.022 0.001 PHE G 26 TRP 0.018 0.002 TRP I 106 HIS 0.018 0.002 HIS G 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 (44474) covalent geometry : angle 0.56292 / 0.30 (60368) hydrogen bonds : bond 0.04261 / 2.89 ( 2434) hydrogen bonds : angle 4.02144 / 2.91 ( 7039) metal coordination : bond 0.04502 / 3.45 ( 64) metal coordination : angle 6.29541 / 4.50 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10116 Ramachandran restraints generated. 5058 Oldfield, 0 Emsley, 5058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10116 Ramachandran restraints generated. 5058 Oldfield, 0 Emsley, 5058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1221 residues out of total 4576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 209 poor density : 1012 time to evaluate : 1.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7549 (tt0) REVERT: A 149 SER cc_start: 0.8221 (m) cc_final: 0.7989 (m) REVERT: A 267 LYS cc_start: 0.8908 (pttt) cc_final: 0.8699 (pttp) REVERT: B 25 GLU cc_start: 0.7349 (tm-30) cc_final: 0.6937 (tm-30) REVERT: B 68 THR cc_start: 0.8495 (t) cc_final: 0.8214 (m) REVERT: B 262 LEU cc_start: 0.6889 (OUTLIER) cc_final: 0.6494 (mm) REVERT: C 9 GLU cc_start: 0.8157 (tt0) cc_final: 0.7943 (tt0) REVERT: C 24 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8304 (mp) REVERT: C 25 GLU cc_start: 0.7604 (tm-30) cc_final: 0.7035 (tm-30) REVERT: C 34 GLU cc_start: 0.8028 (tp30) cc_final: 0.7388 (tp30) REVERT: C 76 LEU cc_start: 0.7166 (mt) cc_final: 0.6948 (mm) REVERT: C 268 ASP cc_start: 0.7202 (t0) cc_final: 0.6693 (t0) REVERT: D 109 MET cc_start: 0.7042 (mmm) cc_final: 0.6741 (tpp) REVERT: D 132 MET cc_start: 0.5960 (ppp) cc_final: 0.5551 (ppp) REVERT: D 188 LYS cc_start: 0.7435 (mmtt) cc_final: 0.6840 (mmtt) REVERT: D 207 GLN cc_start: 0.7333 (OUTLIER) cc_final: 0.6939 (mp10) REVERT: E 1 TRP cc_start: 0.4873 (m-90) cc_final: 0.2951 (m-90) REVERT: E 137 ILE cc_start: 0.8291 (mm) cc_final: 0.7798 (mm) REVERT: E 207 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.8171 (mm110) REVERT: F 150 GLN cc_start: 0.7826 (mt0) cc_final: 0.7539 (mt0) REVERT: F 199 ASP cc_start: 0.7636 (m-30) cc_final: 0.7277 (m-30) REVERT: F 206 GLU cc_start: 0.8053 (tp30) cc_final: 0.7528 (tp30) REVERT: F 209 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.7343 (tmm160) REVERT: G 24 LEU cc_start: 0.8781 (mt) cc_final: 0.8508 (mp) REVERT: G 80 GLU cc_start: 0.7337 (tm-30) cc_final: 0.6632 (tm-30) REVERT: G 104 MET cc_start: 0.8539 (mmm) cc_final: 0.8337 (mmm) REVERT: G 131 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8523 (tp) REVERT: G 161 LYS cc_start: 0.8718 (mttt) cc_final: 0.8473 (mttt) REVERT: G 165 GLU cc_start: 0.8063 (tp30) cc_final: 0.7616 (tp30) REVERT: G 184 THR cc_start: 0.8397 (OUTLIER) cc_final: 0.8188 (m) REVERT: G 208 GLN cc_start: 0.8226 (tm-30) cc_final: 0.7946 (tm-30) REVERT: H 10 GLU cc_start: 0.7070 (tp30) cc_final: 0.6758 (tp30) REVERT: H 14 LYS cc_start: 0.8689 (mtmt) cc_final: 0.7881 (mtmt) REVERT: H 17 GLN cc_start: 0.8226 (pm20) cc_final: 0.7943 (pm20) REVERT: H 34 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7441 (mt-10) REVERT: H 38 GLN cc_start: 0.8684 (mm-40) cc_final: 0.8433 (mm-40) REVERT: H 48 MET cc_start: 0.7089 (ppp) cc_final: 0.6862 (ppp) REVERT: H 76 LEU cc_start: 0.7902 (tp) cc_final: 0.7617 (tm) REVERT: H 109 MET cc_start: 0.7276 (pmm) cc_final: 0.7069 (pmm) REVERT: H 170 MET cc_start: 0.6670 (OUTLIER) cc_final: 0.6370 (tmm) REVERT: H 243 VAL cc_start: 0.8479 (t) cc_final: 0.8265 (p) REVERT: H 254 LYS cc_start: 0.7536 (OUTLIER) cc_final: 0.7334 (ttmm) REVERT: a 387 MET cc_start: 0.7041 (mtm) cc_final: 0.6782 (tpp) REVERT: a 413 MET cc_start: 0.6317 (mtp) cc_final: 0.6027 (mtp) REVERT: b 426 MET cc_start: 0.4281 (ttm) cc_final: 0.3753 (ttp) REVERT: d 348 MET cc_start: 0.7043 (tpp) cc_final: 0.6529 (tpp) REVERT: e 413 MET cc_start: 0.6156 (mtp) cc_final: 0.5936 (mtp) REVERT: f 396 MET cc_start: 0.8533 (ttp) cc_final: 0.8144 (ttp) REVERT: I 168 ILE cc_start: 0.8796 (OUTLIER) cc_final: 0.8376 (mp) REVERT: I 241 THR cc_start: 0.7921 (t) cc_final: 0.7702 (p) REVERT: I 259 ASP cc_start: 0.7176 (t0) cc_final: 0.6907 (t0) REVERT: J 25 GLU cc_start: 0.7361 (tm-30) cc_final: 0.7000 (tm-30) REVERT: J 68 THR cc_start: 0.8498 (t) cc_final: 0.8199 (m) REVERT: J 124 VAL cc_start: 0.8102 (t) cc_final: 0.7842 (m) REVERT: J 132 MET cc_start: 0.8828 (tpp) cc_final: 0.8621 (mmt) REVERT: J 207 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7516 (mp10) REVERT: J 262 LEU cc_start: 0.7338 (OUTLIER) cc_final: 0.7054 (mm) REVERT: K 25 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7206 (tm-30) REVERT: K 34 GLU cc_start: 0.8227 (tp30) cc_final: 0.7924 (tp30) REVERT: K 166 LYS cc_start: 0.8656 (pttt) cc_final: 0.8398 (pttt) REVERT: K 193 LEU cc_start: 0.8760 (mt) cc_final: 0.8535 (mp) REVERT: K 262 LEU cc_start: 0.7982 (mm) cc_final: 0.7703 (mm) REVERT: K 268 ASP cc_start: 0.7475 (t0) cc_final: 0.6999 (t0) REVERT: L 132 MET cc_start: 0.6232 (ppp) cc_final: 0.5754 (ppp) REVERT: L 188 LYS cc_start: 0.7183 (mmtt) cc_final: 0.6738 (mmtt) REVERT: L 207 GLN cc_start: 0.7303 (OUTLIER) cc_final: 0.6820 (mp10) REVERT: M 1 TRP cc_start: 0.4839 (m-90) cc_final: 0.2681 (m-90) REVERT: M 34 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7654 (mm-30) REVERT: M 48 MET cc_start: 0.2693 (tpt) cc_final: 0.1834 (tpt) REVERT: M 61 ASP cc_start: 0.7577 (t0) cc_final: 0.7298 (t70) REVERT: M 80 GLU cc_start: 0.7410 (tm-30) cc_final: 0.7161 (tm-30) REVERT: M 107 TYR cc_start: 0.7938 (t80) cc_final: 0.7614 (t80) REVERT: M 255 ASP cc_start: 0.7963 (t0) cc_final: 0.7717 (t0) REVERT: N 4 ASN cc_start: 0.7389 (p0) cc_final: 0.6965 (p0) REVERT: N 28 ILE cc_start: 0.8435 (pt) cc_final: 0.8041 (mm) REVERT: N 113 LYS cc_start: 0.8549 (mmmt) cc_final: 0.8316 (mmmt) REVERT: N 146 ASN cc_start: 0.6261 (OUTLIER) cc_final: 0.5870 (t0) REVERT: N 150 GLN cc_start: 0.7826 (mt0) cc_final: 0.7571 (mt0) REVERT: N 162 ASN cc_start: 0.8044 (m110) cc_final: 0.7675 (m110) REVERT: N 199 ASP cc_start: 0.7690 (m-30) cc_final: 0.7340 (m-30) REVERT: N 231 ARG cc_start: 0.7841 (mtp-110) cc_final: 0.7570 (mtp-110) REVERT: O 80 GLU cc_start: 0.7224 (tm-30) cc_final: 0.6811 (mm-30) REVERT: O 109 MET cc_start: 0.8037 (ptm) cc_final: 0.7764 (ptm) REVERT: O 161 LYS cc_start: 0.8568 (mttt) cc_final: 0.8361 (mttt) REVERT: O 164 LEU cc_start: 0.8162 (tp) cc_final: 0.7806 (tm) REVERT: O 165 GLU cc_start: 0.8191 (tp30) cc_final: 0.7667 (tp30) REVERT: O 170 MET cc_start: 0.6643 (mmt) cc_final: 0.6377 (mmt) REVERT: O 184 THR cc_start: 0.8420 (OUTLIER) cc_final: 0.8212 (m) REVERT: O 208 GLN cc_start: 0.8206 (tm-30) cc_final: 0.7778 (tm-30) REVERT: P 10 GLU cc_start: 0.7499 (tp30) cc_final: 0.7176 (tp30) REVERT: P 14 LYS cc_start: 0.8645 (mtmt) cc_final: 0.7686 (mtmt) REVERT: P 48 MET cc_start: 0.4429 (ppp) cc_final: 0.3986 (ppp) REVERT: P 85 LEU cc_start: 0.8811 (tp) cc_final: 0.8593 (tt) REVERT: P 166 LYS cc_start: 0.8666 (ttpp) cc_final: 0.8434 (mtpp) REVERT: P 221 ILE cc_start: 0.8179 (OUTLIER) cc_final: 0.7973 (mm) REVERT: P 254 LYS cc_start: 0.7590 (ttmm) cc_final: 0.7390 (tptm) REVERT: P 276 LYS cc_start: 0.5666 (OUTLIER) cc_final: 0.4285 (mtmt) REVERT: h 426 MET cc_start: 0.3659 (ttm) cc_final: 0.2715 (ttt) REVERT: k 387 MET cc_start: 0.7885 (mmm) cc_final: 0.7036 (tpt) REVERT: l 348 MET cc_start: 0.4232 (tpp) cc_final: 0.3972 (tpp) REVERT: l 387 MET cc_start: 0.6558 (mtm) cc_final: 0.6298 (mtm) REVERT: l 426 MET cc_start: 0.2256 (ttm) cc_final: 0.1931 (ttm) outliers start: 209 outliers final: 103 residues processed: 1096 average time/residue: 0.8194 time to fit residues: 1086.4255 Evaluate side-chains 1114 residues out of total 4576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 992 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 TRP Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain C residue 3 GLU Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 92 LYS Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 207 GLN Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 207 GLN Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain F residue 16 HIS Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 187 ILE Chi-restraints excluded: chain F residue 195 THR Chi-restraints excluded: chain F residue 209 ARG Chi-restraints excluded: chain G residue 11 GLU Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain G residue 260 ARG Chi-restraints excluded: chain H residue 23 HIS Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain H residue 170 MET Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 198 MET Chi-restraints excluded: chain H residue 254 LYS Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain a residue 418 MET Chi-restraints excluded: chain d residue 403 ILE Chi-restraints excluded: chain I residue 1 TRP Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 133 LYS Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 168 ILE Chi-restraints excluded: chain I residue 190 LYS Chi-restraints excluded: chain I residue 227 ARG Chi-restraints excluded: chain I residue 251 ILE Chi-restraints excluded: chain I residue 253 VAL Chi-restraints excluded: chain J residue 17 GLN Chi-restraints excluded: chain J residue 92 LYS Chi-restraints excluded: chain J residue 94 GLU Chi-restraints excluded: chain J residue 133 LYS Chi-restraints excluded: chain J residue 137 ILE Chi-restraints excluded: chain J residue 138 GLU Chi-restraints excluded: chain J residue 168 ILE Chi-restraints excluded: chain J residue 193 LEU Chi-restraints excluded: chain J residue 207 GLN Chi-restraints excluded: chain J residue 262 LEU Chi-restraints excluded: chain K residue 25 GLU Chi-restraints excluded: chain K residue 104 MET Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 205 LYS Chi-restraints excluded: chain K residue 241 THR Chi-restraints excluded: chain K residue 252 VAL Chi-restraints excluded: chain L residue 127 SER Chi-restraints excluded: chain L residue 207 GLN Chi-restraints excluded: chain L residue 253 VAL Chi-restraints excluded: chain L residue 264 ILE Chi-restraints excluded: chain M residue 10 GLU Chi-restraints excluded: chain M residue 17 GLN Chi-restraints excluded: chain M residue 92 LYS Chi-restraints excluded: chain M residue 207 GLN Chi-restraints excluded: chain M residue 210 ILE Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 264 ILE Chi-restraints excluded: chain M residue 276 LYS Chi-restraints excluded: chain N residue 44 GLN Chi-restraints excluded: chain N residue 91 VAL Chi-restraints excluded: chain N residue 131 LEU Chi-restraints excluded: chain N residue 133 LYS Chi-restraints excluded: chain N residue 143 ILE Chi-restraints excluded: chain N residue 146 ASN Chi-restraints excluded: chain N residue 155 ARG Chi-restraints excluded: chain N residue 168 ILE Chi-restraints excluded: chain N residue 195 THR Chi-restraints excluded: chain N residue 244 LEU Chi-restraints excluded: chain N residue 251 ILE Chi-restraints excluded: chain O residue 11 GLU Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 184 THR Chi-restraints excluded: chain O residue 200 ILE Chi-restraints excluded: chain O residue 260 ARG Chi-restraints excluded: chain O residue 264 ILE Chi-restraints excluded: chain P residue 18 ASP Chi-restraints excluded: chain P residue 23 HIS Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 131 LEU Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain P residue 162 ASN Chi-restraints excluded: chain P residue 164 LEU Chi-restraints excluded: chain P residue 183 ILE Chi-restraints excluded: chain P residue 185 LEU Chi-restraints excluded: chain P residue 193 LEU Chi-restraints excluded: chain P residue 221 ILE Chi-restraints excluded: chain P residue 252 VAL Chi-restraints excluded: chain P residue 263 VAL Chi-restraints excluded: chain P residue 276 LYS Chi-restraints excluded: chain g residue 396 MET Chi-restraints excluded: chain h residue 387 MET Chi-restraints excluded: chain i residue 426 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 184 optimal weight: 0.3980 chunk 336 optimal weight: 7.9990 chunk 287 optimal weight: 0.0970 chunk 46 optimal weight: 0.9980 chunk 188 optimal weight: 3.9990 chunk 213 optimal weight: 9.9990 chunk 414 optimal weight: 2.9990 chunk 501 optimal weight: 0.9980 chunk 454 optimal weight: 1.9990 chunk 490 optimal weight: 2.9990 chunk 398 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 GLN A 266 ASN B 17 GLN ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 HIS E 242 GLN ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 23 HIS F 56 ASN ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 HIS ** F 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 172 ASN F 266 ASN ** G 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 GLN ** I 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 148 GLN I 150 GLN I 213 GLN I 238 GLN J 129 GLN ** K 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 139 HIS M 213 GLN M 242 GLN ** N 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 69 HIS N 82 ASN ** N 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 204 ASN N 266 ASN O 82 ASN O 162 ASN ** P 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 204 ASN k 367 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.207323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.155982 restraints weight = 65265.391| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 2.77 r_work: 0.3655 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.227 44538 Z= 0.166 Angle : 0.583 15.649 60392 Z= 0.303 Chirality : 0.043 0.229 6606 Planarity : 0.004 0.061 7462 Dihedral : 13.169 75.261 6366 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.49 % Allowed : 16.45 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.12), residues: 5058 helix: 2.37 (0.10), residues: 2682 sheet: 0.45 (0.17), residues: 908 loop : -1.20 (0.15), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG H 189 TYR 0.026 0.002 TYR O 225 PHE 0.019 0.001 PHE E 201 TRP 0.018 0.002 TRP A 106 HIS 0.018 0.001 HIS G 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 (44474) covalent geometry : angle 0.57133 / 0.30 (60368) hydrogen bonds : bond 0.04163 / 2.82 ( 2434) hydrogen bonds : angle 4.00897 / 2.90 ( 7039) metal coordination : bond 0.04837 / 3.63 ( 64) metal coordination : angle 5.94373 / 4.20 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10116 Ramachandran restraints generated. 5058 Oldfield, 0 Emsley, 5058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10116 Ramachandran restraints generated. 5058 Oldfield, 0 Emsley, 5058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1217 residues out of total 4576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 204 poor density : 1013 time to evaluate : 1.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7608 (tm-30) REVERT: A 98 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7369 (mm-30) REVERT: A 149 SER cc_start: 0.8199 (m) cc_final: 0.7955 (m) REVERT: A 227 ARG cc_start: 0.8119 (ptt180) cc_final: 0.7372 (ptm-80) REVERT: B 25 GLU cc_start: 0.7381 (tm-30) cc_final: 0.6941 (tm-30) REVERT: B 68 THR cc_start: 0.8467 (t) cc_final: 0.8189 (m) REVERT: B 207 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7953 (mm-40) REVERT: B 262 LEU cc_start: 0.6926 (OUTLIER) cc_final: 0.6518 (mm) REVERT: C 9 GLU cc_start: 0.8146 (tt0) cc_final: 0.7919 (tt0) REVERT: C 24 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8297 (mp) REVERT: C 25 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7009 (tm-30) REVERT: C 34 GLU cc_start: 0.8010 (tp30) cc_final: 0.7394 (tp30) REVERT: C 76 LEU cc_start: 0.7172 (mt) cc_final: 0.6958 (mm) REVERT: C 268 ASP cc_start: 0.7235 (t0) cc_final: 0.6735 (t0) REVERT: D 188 LYS cc_start: 0.7427 (mmtt) cc_final: 0.6816 (mmtt) REVERT: D 207 GLN cc_start: 0.7342 (OUTLIER) cc_final: 0.6937 (mp10) REVERT: E 1 TRP cc_start: 0.4891 (m-90) cc_final: 0.2776 (m-90) REVERT: E 256 ARG cc_start: 0.7418 (mmp80) cc_final: 0.7136 (mmp80) REVERT: F 199 ASP cc_start: 0.7598 (m-30) cc_final: 0.7248 (m-30) REVERT: F 206 GLU cc_start: 0.8015 (tp30) cc_final: 0.7518 (tp30) REVERT: F 209 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.7340 (tmm160) REVERT: G 24 LEU cc_start: 0.8772 (mt) cc_final: 0.8517 (mp) REVERT: G 80 GLU cc_start: 0.7218 (tm-30) cc_final: 0.6651 (tm-30) REVERT: G 104 MET cc_start: 0.8500 (mmm) cc_final: 0.8275 (mmm) REVERT: G 161 LYS cc_start: 0.8696 (mttt) cc_final: 0.8457 (mttt) REVERT: G 165 GLU cc_start: 0.8048 (tp30) cc_final: 0.7540 (tp30) REVERT: G 208 GLN cc_start: 0.8228 (tm-30) cc_final: 0.7957 (tm-30) REVERT: G 262 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7568 (mm) REVERT: H 10 GLU cc_start: 0.7039 (tp30) cc_final: 0.6734 (tp30) REVERT: H 14 LYS cc_start: 0.8657 (mtmt) cc_final: 0.7840 (mtmt) REVERT: H 34 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7440 (mt-10) REVERT: H 48 MET cc_start: 0.7135 (ppp) cc_final: 0.6929 (ppp) REVERT: H 76 LEU cc_start: 0.7912 (tp) cc_final: 0.7625 (tm) REVERT: H 79 VAL cc_start: 0.7221 (OUTLIER) cc_final: 0.6911 (p) REVERT: H 170 MET cc_start: 0.6652 (OUTLIER) cc_final: 0.6366 (tmm) REVERT: H 254 LYS cc_start: 0.7600 (OUTLIER) cc_final: 0.7368 (ttmm) REVERT: a 387 MET cc_start: 0.7082 (mtm) cc_final: 0.6822 (tpp) REVERT: a 413 MET cc_start: 0.6312 (mtp) cc_final: 0.6013 (mtp) REVERT: b 426 MET cc_start: 0.4294 (ttm) cc_final: 0.4060 (ttp) REVERT: d 348 MET cc_start: 0.7037 (tpp) cc_final: 0.6511 (tpp) REVERT: d 413 MET cc_start: 0.7261 (mmt) cc_final: 0.7006 (mmt) REVERT: f 396 MET cc_start: 0.8554 (ttp) cc_final: 0.8154 (ttp) REVERT: I 168 ILE cc_start: 0.8790 (OUTLIER) cc_final: 0.8354 (mp) REVERT: I 259 ASP cc_start: 0.7178 (t0) cc_final: 0.6958 (t0) REVERT: J 25 GLU cc_start: 0.7343 (tm-30) cc_final: 0.6969 (tm-30) REVERT: J 68 THR cc_start: 0.8488 (t) cc_final: 0.8177 (m) REVERT: J 124 VAL cc_start: 0.8111 (t) cc_final: 0.7871 (m) REVERT: J 132 MET cc_start: 0.8791 (tpp) cc_final: 0.8585 (mmt) REVERT: J 133 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8231 (mtmt) REVERT: J 207 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7519 (mp10) REVERT: J 262 LEU cc_start: 0.7374 (OUTLIER) cc_final: 0.7068 (mm) REVERT: K 25 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7142 (tm-30) REVERT: K 34 GLU cc_start: 0.8209 (tp30) cc_final: 0.7924 (tp30) REVERT: K 39 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.7652 (mp10) REVERT: K 166 LYS cc_start: 0.8680 (pttt) cc_final: 0.8436 (pttt) REVERT: K 262 LEU cc_start: 0.7942 (mm) cc_final: 0.7657 (mm) REVERT: K 268 ASP cc_start: 0.7500 (t0) cc_final: 0.7000 (t0) REVERT: L 132 MET cc_start: 0.6250 (ppp) cc_final: 0.5762 (ppp) REVERT: L 188 LYS cc_start: 0.7139 (mmtt) cc_final: 0.6753 (mmtt) REVERT: L 207 GLN cc_start: 0.7326 (OUTLIER) cc_final: 0.6823 (mp10) REVERT: M 1 TRP cc_start: 0.4784 (m-90) cc_final: 0.2640 (m-90) REVERT: M 34 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7653 (mm-30) REVERT: M 48 MET cc_start: 0.2728 (tpt) cc_final: 0.1859 (tpt) REVERT: M 107 TYR cc_start: 0.7932 (t80) cc_final: 0.7668 (t80) REVERT: N 4 ASN cc_start: 0.7330 (p0) cc_final: 0.6853 (p0) REVERT: N 28 ILE cc_start: 0.8424 (pt) cc_final: 0.7998 (mm) REVERT: N 113 LYS cc_start: 0.8515 (mmmt) cc_final: 0.8286 (mmmt) REVERT: N 146 ASN cc_start: 0.6325 (OUTLIER) cc_final: 0.5950 (t0) REVERT: N 150 GLN cc_start: 0.7840 (mt0) cc_final: 0.7597 (mt0) REVERT: N 162 ASN cc_start: 0.8026 (m110) cc_final: 0.7656 (m110) REVERT: N 199 ASP cc_start: 0.7618 (m-30) cc_final: 0.7270 (m-30) REVERT: O 9 GLU cc_start: 0.7617 (mm-30) cc_final: 0.7301 (mm-30) REVERT: O 80 GLU cc_start: 0.7110 (tm-30) cc_final: 0.6655 (tm-30) REVERT: O 161 LYS cc_start: 0.8565 (mttt) cc_final: 0.8355 (mttt) REVERT: O 164 LEU cc_start: 0.8105 (tp) cc_final: 0.7795 (tm) REVERT: O 165 GLU cc_start: 0.8153 (tp30) cc_final: 0.7631 (tp30) REVERT: O 208 GLN cc_start: 0.8227 (tm-30) cc_final: 0.7830 (tm-30) REVERT: P 10 GLU cc_start: 0.7435 (tp30) cc_final: 0.6348 (tp30) REVERT: P 14 LYS cc_start: 0.8619 (mtmt) cc_final: 0.7689 (mtmt) REVERT: P 48 MET cc_start: 0.4455 (ppp) cc_final: 0.4023 (ppp) REVERT: P 178 LEU cc_start: 0.8255 (tm) cc_final: 0.7974 (tp) REVERT: P 221 ILE cc_start: 0.8109 (OUTLIER) cc_final: 0.7904 (mm) REVERT: P 276 LYS cc_start: 0.5822 (OUTLIER) cc_final: 0.4428 (mtmt) REVERT: h 426 MET cc_start: 0.3656 (ttm) cc_final: 0.2698 (ttt) REVERT: k 387 MET cc_start: 0.7957 (mmm) cc_final: 0.7121 (tpt) REVERT: k 413 MET cc_start: 0.6119 (mtp) cc_final: 0.5837 (mtp) REVERT: k 415 LYS cc_start: 0.7362 (mmmm) cc_final: 0.6894 (mmmm) REVERT: l 348 MET cc_start: 0.4322 (tpp) cc_final: 0.4052 (tpp) REVERT: l 387 MET cc_start: 0.6544 (mtm) cc_final: 0.6288 (mtm) REVERT: l 426 MET cc_start: 0.2177 (ttm) cc_final: 0.1840 (ttm) outliers start: 204 outliers final: 113 residues processed: 1085 average time/residue: 0.7933 time to fit residues: 1041.0193 Evaluate side-chains 1127 residues out of total 4576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 993 time to evaluate : 1.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 TRP Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 266 ASN Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 207 GLN Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain C residue 3 GLU Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 206 GLU Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 207 GLN Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 80 GLU Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 187 ILE Chi-restraints excluded: chain F residue 195 THR Chi-restraints excluded: chain F residue 209 ARG Chi-restraints excluded: chain G residue 11 GLU Chi-restraints excluded: chain G residue 109 MET Chi-restraints excluded: chain G residue 187 ILE Chi-restraints excluded: chain G residue 260 ARG Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain H residue 23 HIS Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 116 GLN Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain H residue 170 MET Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 198 MET Chi-restraints excluded: chain H residue 252 VAL Chi-restraints excluded: chain H residue 254 LYS Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain a residue 418 MET Chi-restraints excluded: chain d residue 403 ILE Chi-restraints excluded: chain e residue 360 LYS Chi-restraints excluded: chain I residue 1 TRP Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 133 LYS Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 168 ILE Chi-restraints excluded: chain I residue 190 LYS Chi-restraints excluded: chain I residue 227 ARG Chi-restraints excluded: chain I residue 251 ILE Chi-restraints excluded: chain I residue 253 VAL Chi-restraints excluded: chain J residue 17 GLN Chi-restraints excluded: chain J residue 92 LYS Chi-restraints excluded: chain J residue 94 GLU Chi-restraints excluded: chain J residue 133 LYS Chi-restraints excluded: chain J residue 137 ILE Chi-restraints excluded: chain J residue 138 GLU Chi-restraints excluded: chain J residue 168 ILE Chi-restraints excluded: chain J residue 207 GLN Chi-restraints excluded: chain J residue 262 LEU Chi-restraints excluded: chain K residue 3 GLU Chi-restraints excluded: chain K residue 25 GLU Chi-restraints excluded: chain K residue 39 GLN Chi-restraints excluded: chain K residue 104 MET Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 205 LYS Chi-restraints excluded: chain K residue 241 THR Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 252 VAL Chi-restraints excluded: chain L residue 127 SER Chi-restraints excluded: chain L residue 128 THR Chi-restraints excluded: chain L residue 137 ILE Chi-restraints excluded: chain L residue 207 GLN Chi-restraints excluded: chain L residue 253 VAL Chi-restraints excluded: chain L residue 264 ILE Chi-restraints excluded: chain M residue 10 GLU Chi-restraints excluded: chain M residue 89 GLU Chi-restraints excluded: chain M residue 207 GLN Chi-restraints excluded: chain M residue 210 ILE Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 264 ILE Chi-restraints excluded: chain N residue 16 HIS Chi-restraints excluded: chain N residue 25 GLU Chi-restraints excluded: chain N residue 91 VAL Chi-restraints excluded: chain N residue 133 LYS Chi-restraints excluded: chain N residue 143 ILE Chi-restraints excluded: chain N residue 146 ASN Chi-restraints excluded: chain N residue 155 ARG Chi-restraints excluded: chain N residue 168 ILE Chi-restraints excluded: chain N residue 195 THR Chi-restraints excluded: chain N residue 251 ILE Chi-restraints excluded: chain O residue 11 GLU Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 212 GLN Chi-restraints excluded: chain O residue 260 ARG Chi-restraints excluded: chain O residue 264 ILE Chi-restraints excluded: chain P residue 18 ASP Chi-restraints excluded: chain P residue 23 HIS Chi-restraints excluded: chain P residue 34 GLU Chi-restraints excluded: chain P residue 80 GLU Chi-restraints excluded: chain P residue 131 LEU Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain P residue 162 ASN Chi-restraints excluded: chain P residue 183 ILE Chi-restraints excluded: chain P residue 185 LEU Chi-restraints excluded: chain P residue 221 ILE Chi-restraints excluded: chain P residue 252 VAL Chi-restraints excluded: chain P residue 263 VAL Chi-restraints excluded: chain P residue 276 LYS Chi-restraints excluded: chain g residue 396 MET Chi-restraints excluded: chain h residue 387 MET Chi-restraints excluded: chain i residue 426 MET Chi-restraints excluded: chain j residue 359 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 359 optimal weight: 0.9980 chunk 354 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 288 optimal weight: 0.7980 chunk 422 optimal weight: 4.9990 chunk 203 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 327 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 285 optimal weight: 4.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 GLN B 17 GLN ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 HIS E 212 GLN E 242 GLN ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 150 GLN F 266 ASN ** G 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 GLN H 204 ASN ** I 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 148 GLN I 150 GLN I 238 GLN J 129 GLN ** K 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 119 ASN M 212 GLN M 213 GLN M 242 GLN ** N 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 69 HIS N 82 ASN ** N 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 172 ASN N 266 ASN ** O 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 82 ASN O 116 GLN ** O 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 162 ASN P 13 ASN ** P 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.206350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.154896 restraints weight = 64930.806| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 2.41 r_work: 0.3672 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3512 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.246 44538 Z= 0.198 Angle : 0.619 17.625 60392 Z= 0.319 Chirality : 0.044 0.230 6606 Planarity : 0.004 0.062 7462 Dihedral : 13.208 75.856 6364 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.20 % Favored : 96.78 % Rotamer: Outliers : 4.60 % Allowed : 17.29 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.12), residues: 5058 helix: 2.22 (0.10), residues: 2696 sheet: 0.35 (0.17), residues: 912 loop : -1.30 (0.15), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG L 155 TYR 0.047 0.002 TYR O 225 PHE 0.021 0.001 PHE E 201 TRP 0.022 0.002 TRP O 237 HIS 0.021 0.002 HIS G 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.19 (44474) covalent geometry : angle 0.60042 / 0.32 (60368) hydrogen bonds : bond 0.04473 / 3.05 ( 2434) hydrogen bonds : angle 4.02579 / 2.92 ( 7039) metal coordination : bond 0.05670 / 4.08 ( 64) metal coordination : angle 7.57681 / 6.02 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10116 Ramachandran restraints generated. 5058 Oldfield, 0 Emsley, 5058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10116 Ramachandran restraints generated. 5058 Oldfield, 0 Emsley, 5058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1209 residues out of total 4576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 209 poor density : 1000 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7801 (tm-30) REVERT: A 98 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7765 (mm-30) REVERT: A 149 SER cc_start: 0.8331 (m) cc_final: 0.8099 (m) REVERT: B 25 GLU cc_start: 0.7487 (tm-30) cc_final: 0.7031 (tm-30) REVERT: B 68 THR cc_start: 0.8567 (t) cc_final: 0.8294 (m) REVERT: B 207 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.8203 (mm-40) REVERT: B 262 LEU cc_start: 0.6989 (OUTLIER) cc_final: 0.6579 (mm) REVERT: C 25 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7298 (tm-30) REVERT: C 34 GLU cc_start: 0.8272 (tp30) cc_final: 0.7649 (tp30) REVERT: C 76 LEU cc_start: 0.7304 (mt) cc_final: 0.7085 (mm) REVERT: C 268 ASP cc_start: 0.7451 (t0) cc_final: 0.6950 (t0) REVERT: D 109 MET cc_start: 0.7185 (mmm) cc_final: 0.6842 (tpp) REVERT: D 188 LYS cc_start: 0.7643 (mmtt) cc_final: 0.7036 (mmtt) REVERT: D 207 GLN cc_start: 0.7300 (OUTLIER) cc_final: 0.6897 (mp10) REVERT: E 1 TRP cc_start: 0.5127 (m-90) cc_final: 0.3037 (m-90) REVERT: E 104 MET cc_start: 0.8452 (ttm) cc_final: 0.8128 (mtp) REVERT: E 256 ARG cc_start: 0.7687 (mmp80) cc_final: 0.7431 (mmp80) REVERT: F 199 ASP cc_start: 0.7916 (m-30) cc_final: 0.7562 (m-30) REVERT: F 206 GLU cc_start: 0.8311 (tp30) cc_final: 0.7852 (tp30) REVERT: F 209 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.7511 (tmm160) REVERT: G 24 LEU cc_start: 0.8835 (mt) cc_final: 0.8587 (mp) REVERT: G 80 GLU cc_start: 0.7513 (tm-30) cc_final: 0.7005 (tm-30) REVERT: G 82 ASN cc_start: 0.7746 (m110) cc_final: 0.7432 (m110) REVERT: G 104 MET cc_start: 0.8688 (mmm) cc_final: 0.8474 (mmm) REVERT: G 161 LYS cc_start: 0.8780 (mttt) cc_final: 0.8573 (mttt) REVERT: G 165 GLU cc_start: 0.8272 (tp30) cc_final: 0.7795 (tp30) REVERT: G 208 GLN cc_start: 0.8443 (tm-30) cc_final: 0.8160 (tm-30) REVERT: G 262 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7559 (mm) REVERT: H 10 GLU cc_start: 0.7255 (tp30) cc_final: 0.6893 (tp30) REVERT: H 14 LYS cc_start: 0.8632 (mtmt) cc_final: 0.7881 (mtmt) REVERT: H 34 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7473 (mt-10) REVERT: H 48 MET cc_start: 0.7121 (ppp) cc_final: 0.6905 (ppp) REVERT: H 76 LEU cc_start: 0.8066 (tp) cc_final: 0.7806 (tm) REVERT: H 79 VAL cc_start: 0.7500 (OUTLIER) cc_final: 0.7203 (p) REVERT: H 94 GLU cc_start: 0.7921 (mp0) cc_final: 0.7691 (mm-30) REVERT: H 170 MET cc_start: 0.6884 (OUTLIER) cc_final: 0.6613 (tmm) REVERT: H 185 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7565 (tm) REVERT: H 222 ARG cc_start: 0.6835 (mtp85) cc_final: 0.6591 (mtm180) REVERT: H 254 LYS cc_start: 0.7763 (OUTLIER) cc_final: 0.7532 (ttmm) REVERT: a 387 MET cc_start: 0.7138 (mtm) cc_final: 0.6877 (tpp) REVERT: a 413 MET cc_start: 0.6446 (mtp) cc_final: 0.6104 (mtp) REVERT: b 348 MET cc_start: 0.4200 (ppp) cc_final: 0.2363 (ttm) REVERT: b 426 MET cc_start: 0.4515 (ttm) cc_final: 0.4046 (ttp) REVERT: d 348 MET cc_start: 0.7140 (tpp) cc_final: 0.6594 (tpp) REVERT: e 415 LYS cc_start: 0.7758 (mmmm) cc_final: 0.7340 (mmmm) REVERT: f 396 MET cc_start: 0.8532 (ttp) cc_final: 0.8128 (ttp) REVERT: J 25 GLU cc_start: 0.7475 (tm-30) cc_final: 0.7077 (tm-30) REVERT: J 68 THR cc_start: 0.8562 (t) cc_final: 0.8273 (m) REVERT: J 124 VAL cc_start: 0.8253 (t) cc_final: 0.8040 (m) REVERT: J 133 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8365 (mtmt) REVERT: J 207 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.7806 (mp10) REVERT: J 262 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.7176 (mm) REVERT: K 25 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7529 (tm-30) REVERT: K 34 GLU cc_start: 0.8481 (tp30) cc_final: 0.8168 (tp30) REVERT: K 166 LYS cc_start: 0.8828 (pttt) cc_final: 0.8592 (pttt) REVERT: K 262 LEU cc_start: 0.8120 (mm) cc_final: 0.7852 (mm) REVERT: K 268 ASP cc_start: 0.7721 (t0) cc_final: 0.7201 (t0) REVERT: L 132 MET cc_start: 0.6574 (ppp) cc_final: 0.6060 (ppp) REVERT: L 166 LYS cc_start: 0.8207 (ptmt) cc_final: 0.7807 (ptpp) REVERT: L 188 LYS cc_start: 0.7290 (mmtt) cc_final: 0.6623 (mmtm) REVERT: L 207 GLN cc_start: 0.7336 (OUTLIER) cc_final: 0.6841 (mp10) REVERT: M 1 TRP cc_start: 0.5061 (m-90) cc_final: 0.2824 (m-90) REVERT: M 34 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7998 (mm-30) REVERT: M 48 MET cc_start: 0.2610 (tpt) cc_final: 0.1864 (tpt) REVERT: M 107 TYR cc_start: 0.8072 (t80) cc_final: 0.7784 (t80) REVERT: N 4 ASN cc_start: 0.7352 (p0) cc_final: 0.6831 (p0) REVERT: N 28 ILE cc_start: 0.8498 (pt) cc_final: 0.8044 (mm) REVERT: N 113 LYS cc_start: 0.8670 (mmmt) cc_final: 0.8444 (mmmt) REVERT: N 146 ASN cc_start: 0.6577 (OUTLIER) cc_final: 0.6249 (t0) REVERT: N 162 ASN cc_start: 0.8250 (m110) cc_final: 0.7990 (m110) REVERT: N 199 ASP cc_start: 0.8018 (m-30) cc_final: 0.7677 (m-30) REVERT: O 164 LEU cc_start: 0.8149 (tp) cc_final: 0.7871 (tm) REVERT: O 165 GLU cc_start: 0.8274 (tp30) cc_final: 0.7657 (tp30) REVERT: O 166 LYS cc_start: 0.8883 (mttt) cc_final: 0.8439 (mtmm) REVERT: O 208 GLN cc_start: 0.8460 (tm-30) cc_final: 0.8074 (tm-30) REVERT: O 225 TYR cc_start: 0.7504 (t80) cc_final: 0.7129 (t80) REVERT: P 48 MET cc_start: 0.4650 (ppp) cc_final: 0.4181 (ppp) REVERT: P 178 LEU cc_start: 0.8355 (tm) cc_final: 0.8053 (tp) REVERT: P 276 LYS cc_start: 0.6133 (OUTLIER) cc_final: 0.4710 (mtmt) REVERT: h 426 MET cc_start: 0.3774 (ttm) cc_final: 0.2777 (ttt) REVERT: k 413 MET cc_start: 0.6334 (mtp) cc_final: 0.6070 (mtp) REVERT: k 415 LYS cc_start: 0.7526 (mmmm) cc_final: 0.7132 (mmmm) REVERT: l 348 MET cc_start: 0.4376 (tpp) cc_final: 0.4084 (tpp) REVERT: l 387 MET cc_start: 0.6542 (mtm) cc_final: 0.6281 (mtm) REVERT: l 426 MET cc_start: 0.2239 (ttm) cc_final: 0.1895 (ttm) outliers start: 209 outliers final: 134 residues processed: 1084 average time/residue: 0.6745 time to fit residues: 884.4188 Evaluate side-chains 1131 residues out of total 4576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 979 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 TRP Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 190 LYS Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 207 GLN Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain C residue 3 GLU Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 206 GLU Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 207 GLN Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 80 GLU Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 139 HIS Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 252 VAL Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain F residue 16 HIS Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 80 GLU Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 187 ILE Chi-restraints excluded: chain F residue 195 THR Chi-restraints excluded: chain F residue 209 ARG Chi-restraints excluded: chain G residue 11 GLU Chi-restraints excluded: chain G residue 184 THR Chi-restraints excluded: chain G residue 260 ARG Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain H residue 23 HIS Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 116 GLN Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain H residue 170 MET Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 198 MET Chi-restraints excluded: chain H residue 252 VAL Chi-restraints excluded: chain H residue 254 LYS Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain H residue 264 ILE Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain a residue 418 MET Chi-restraints excluded: chain b residue 387 MET Chi-restraints excluded: chain d residue 369 ASP Chi-restraints excluded: chain d residue 403 ILE Chi-restraints excluded: chain e residue 360 LYS Chi-restraints excluded: chain I residue 1 TRP Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 98 GLU Chi-restraints excluded: chain I residue 133 LYS Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 168 ILE Chi-restraints excluded: chain I residue 190 LYS Chi-restraints excluded: chain I residue 227 ARG Chi-restraints excluded: chain I residue 251 ILE Chi-restraints excluded: chain I residue 253 VAL Chi-restraints excluded: chain I residue 258 THR Chi-restraints excluded: chain J residue 42 VAL Chi-restraints excluded: chain J residue 92 LYS Chi-restraints excluded: chain J residue 94 GLU Chi-restraints excluded: chain J residue 133 LYS Chi-restraints excluded: chain J residue 137 ILE Chi-restraints excluded: chain J residue 138 GLU Chi-restraints excluded: chain J residue 168 ILE Chi-restraints excluded: chain J residue 207 GLN Chi-restraints excluded: chain J residue 262 LEU Chi-restraints excluded: chain K residue 3 GLU Chi-restraints excluded: chain K residue 25 GLU Chi-restraints excluded: chain K residue 104 MET Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 205 LYS Chi-restraints excluded: chain K residue 208 GLN Chi-restraints excluded: chain K residue 241 THR Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain K residue 252 VAL Chi-restraints excluded: chain L residue 127 SER Chi-restraints excluded: chain L residue 128 THR Chi-restraints excluded: chain L residue 137 ILE Chi-restraints excluded: chain L residue 207 GLN Chi-restraints excluded: chain L residue 253 VAL Chi-restraints excluded: chain L residue 264 ILE Chi-restraints excluded: chain M residue 10 GLU Chi-restraints excluded: chain M residue 17 GLN Chi-restraints excluded: chain M residue 89 GLU Chi-restraints excluded: chain M residue 105 LYS Chi-restraints excluded: chain M residue 119 ASN Chi-restraints excluded: chain M residue 168 ILE Chi-restraints excluded: chain M residue 207 GLN Chi-restraints excluded: chain M residue 210 ILE Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 272 ILE Chi-restraints excluded: chain N residue 16 HIS Chi-restraints excluded: chain N residue 25 GLU Chi-restraints excluded: chain N residue 91 VAL Chi-restraints excluded: chain N residue 132 MET Chi-restraints excluded: chain N residue 133 LYS Chi-restraints excluded: chain N residue 143 ILE Chi-restraints excluded: chain N residue 146 ASN Chi-restraints excluded: chain N residue 155 ARG Chi-restraints excluded: chain N residue 168 ILE Chi-restraints excluded: chain N residue 195 THR Chi-restraints excluded: chain N residue 251 ILE Chi-restraints excluded: chain O residue 11 GLU Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 184 THR Chi-restraints excluded: chain O residue 187 ILE Chi-restraints excluded: chain O residue 200 ILE Chi-restraints excluded: chain O residue 212 GLN Chi-restraints excluded: chain O residue 251 ILE Chi-restraints excluded: chain O residue 260 ARG Chi-restraints excluded: chain O residue 264 ILE Chi-restraints excluded: chain P residue 18 ASP Chi-restraints excluded: chain P residue 23 HIS Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 80 GLU Chi-restraints excluded: chain P residue 131 LEU Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain P residue 162 ASN Chi-restraints excluded: chain P residue 164 LEU Chi-restraints excluded: chain P residue 183 ILE Chi-restraints excluded: chain P residue 185 LEU Chi-restraints excluded: chain P residue 252 VAL Chi-restraints excluded: chain P residue 263 VAL Chi-restraints excluded: chain P residue 276 LYS Chi-restraints excluded: chain g residue 396 MET Chi-restraints excluded: chain h residue 387 MET Chi-restraints excluded: chain i residue 426 MET Chi-restraints excluded: chain j residue 359 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 256 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 318 optimal weight: 4.9990 chunk 101 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 chunk 475 optimal weight: 0.3980 chunk 116 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 469 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 275 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 GLN ** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 HIS E 242 GLN ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 HIS ** F 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 172 ASN F 266 ASN ** G 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 119 ASN I 148 GLN I 150 GLN I 238 GLN J 17 GLN J 129 GLN ** K 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 242 GLN ** N 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 69 HIS N 82 ASN ** N 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 150 GLN N 266 ASN ** O 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 82 ASN ** O 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 162 ASN ** P 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.207177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.156776 restraints weight = 64585.176| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 2.80 r_work: 0.3653 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.242 44538 Z= 0.148 Angle : 0.615 20.650 60392 Z= 0.314 Chirality : 0.043 0.224 6606 Planarity : 0.004 0.061 7462 Dihedral : 13.190 74.777 6364 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 4.42 % Allowed : 17.84 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.12), residues: 5058 helix: 2.25 (0.10), residues: 2694 sheet: 0.38 (0.17), residues: 908 loop : -1.29 (0.15), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG j 351 TYR 0.026 0.002 TYR O 70 PHE 0.016 0.001 PHE O 26 TRP 0.019 0.001 TRP I 106 HIS 0.025 0.002 HIS G 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (44474) covalent geometry : angle 0.59250 / 0.31 (60368) hydrogen bonds : bond 0.04005 / 2.72 ( 2434) hydrogen bonds : angle 4.00361 / 2.91 ( 7039) metal coordination : bond 0.05651 / 4.37 ( 64) metal coordination : angle 8.36033 / 6.74 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10116 Ramachandran restraints generated. 5058 Oldfield, 0 Emsley, 5058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10116 Ramachandran restraints generated. 5058 Oldfield, 0 Emsley, 5058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1184 residues out of total 4576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 201 poor density : 983 time to evaluate : 1.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 SER cc_start: 0.8161 (m) cc_final: 0.7907 (m) REVERT: A 207 GLN cc_start: 0.8345 (tp40) cc_final: 0.8058 (tp-100) REVERT: B 25 GLU cc_start: 0.7414 (tm-30) cc_final: 0.6972 (tm-30) REVERT: B 68 THR cc_start: 0.8439 (t) cc_final: 0.8174 (m) REVERT: B 207 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7956 (mm-40) REVERT: B 262 LEU cc_start: 0.6931 (OUTLIER) cc_final: 0.6528 (mm) REVERT: C 25 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.6925 (tm-30) REVERT: C 76 LEU cc_start: 0.7218 (mt) cc_final: 0.6994 (mm) REVERT: C 198 MET cc_start: 0.7645 (tpp) cc_final: 0.7436 (mtt) REVERT: C 268 ASP cc_start: 0.7318 (t0) cc_final: 0.6808 (t0) REVERT: D 109 MET cc_start: 0.7055 (mmm) cc_final: 0.6686 (tpp) REVERT: D 188 LYS cc_start: 0.7464 (mmtt) cc_final: 0.6815 (mmtt) REVERT: D 207 GLN cc_start: 0.7333 (OUTLIER) cc_final: 0.6926 (mp10) REVERT: E 1 TRP cc_start: 0.4795 (m-90) cc_final: 0.2704 (m-90) REVERT: F 150 GLN cc_start: 0.7906 (mt0) cc_final: 0.7631 (mt0) REVERT: F 199 ASP cc_start: 0.7565 (m-30) cc_final: 0.7205 (m-30) REVERT: F 206 GLU cc_start: 0.8034 (tp30) cc_final: 0.7537 (tp30) REVERT: F 209 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.7342 (tmm160) REVERT: G 80 GLU cc_start: 0.7272 (tm-30) cc_final: 0.6756 (tm-30) REVERT: G 82 ASN cc_start: 0.7591 (m110) cc_final: 0.7216 (m110) REVERT: G 104 MET cc_start: 0.8463 (mmm) cc_final: 0.8208 (mmm) REVERT: G 161 LYS cc_start: 0.8742 (mttt) cc_final: 0.8540 (mttt) REVERT: G 165 GLU cc_start: 0.8114 (tp30) cc_final: 0.7585 (tp30) REVERT: G 166 LYS cc_start: 0.8644 (mttt) cc_final: 0.8214 (mtmm) REVERT: G 208 GLN cc_start: 0.8253 (tm-30) cc_final: 0.7968 (tm-30) REVERT: G 262 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7566 (mm) REVERT: H 10 GLU cc_start: 0.7069 (tp30) cc_final: 0.6776 (tp30) REVERT: H 14 LYS cc_start: 0.8575 (mtmt) cc_final: 0.7698 (mtmt) REVERT: H 17 GLN cc_start: 0.8002 (pm20) cc_final: 0.7791 (pm20) REVERT: H 34 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7391 (mt-10) REVERT: H 36 ILE cc_start: 0.8278 (mm) cc_final: 0.7800 (tp) REVERT: H 48 MET cc_start: 0.7130 (ppp) cc_final: 0.6908 (ppp) REVERT: H 61 ASP cc_start: 0.7480 (OUTLIER) cc_final: 0.7247 (t70) REVERT: H 76 LEU cc_start: 0.7940 (tp) cc_final: 0.7667 (tm) REVERT: H 79 VAL cc_start: 0.7542 (OUTLIER) cc_final: 0.7231 (p) REVERT: H 82 ASN cc_start: 0.8796 (t0) cc_final: 0.8449 (t0) REVERT: H 94 GLU cc_start: 0.7799 (mp0) cc_final: 0.7582 (mp0) REVERT: H 185 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7439 (tm) REVERT: H 222 ARG cc_start: 0.6690 (mtp85) cc_final: 0.6440 (mtm180) REVERT: H 254 LYS cc_start: 0.7640 (OUTLIER) cc_final: 0.7403 (ttmm) REVERT: a 387 MET cc_start: 0.7077 (mtm) cc_final: 0.6822 (tpp) REVERT: a 413 MET cc_start: 0.6388 (mtp) cc_final: 0.6047 (mtp) REVERT: b 426 MET cc_start: 0.4374 (ttm) cc_final: 0.4145 (ttp) REVERT: c 415 LYS cc_start: 0.6766 (mtpt) cc_final: 0.6537 (tttm) REVERT: d 348 MET cc_start: 0.7153 (tpp) cc_final: 0.6545 (tpp) REVERT: f 396 MET cc_start: 0.8533 (ttp) cc_final: 0.8139 (ttp) REVERT: I 133 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8453 (ttmm) REVERT: I 253 VAL cc_start: 0.8322 (OUTLIER) cc_final: 0.8030 (p) REVERT: J 25 GLU cc_start: 0.7369 (tm-30) cc_final: 0.6960 (tm-30) REVERT: J 68 THR cc_start: 0.8441 (t) cc_final: 0.8147 (m) REVERT: J 124 VAL cc_start: 0.8110 (t) cc_final: 0.7899 (m) REVERT: J 133 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.8250 (mtmt) REVERT: J 207 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7546 (mp10) REVERT: J 262 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.7077 (mm) REVERT: K 34 GLU cc_start: 0.8171 (tp30) cc_final: 0.7824 (tp30) REVERT: K 262 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7687 (mm) REVERT: K 268 ASP cc_start: 0.7581 (t0) cc_final: 0.7062 (t0) REVERT: L 132 MET cc_start: 0.6301 (ppp) cc_final: 0.5798 (ppp) REVERT: L 166 LYS cc_start: 0.8229 (ptmt) cc_final: 0.7803 (pttt) REVERT: L 188 LYS cc_start: 0.7137 (mmtt) cc_final: 0.6761 (mmtt) REVERT: L 207 GLN cc_start: 0.7330 (OUTLIER) cc_final: 0.6943 (mp10) REVERT: M 1 TRP cc_start: 0.4782 (m-90) cc_final: 0.2621 (m-90) REVERT: M 48 MET cc_start: 0.2718 (tpt) cc_final: 0.1878 (tpt) REVERT: M 107 TYR cc_start: 0.7914 (t80) cc_final: 0.7679 (t80) REVERT: N 113 LYS cc_start: 0.8523 (mmmt) cc_final: 0.8289 (mmmt) REVERT: N 162 ASN cc_start: 0.8034 (m110) cc_final: 0.7777 (m110) REVERT: N 199 ASP cc_start: 0.7647 (m-30) cc_final: 0.7281 (m-30) REVERT: N 251 ILE cc_start: 0.8265 (OUTLIER) cc_final: 0.8057 (pt) REVERT: O 9 GLU cc_start: 0.7682 (mm-30) cc_final: 0.7349 (mm-30) REVERT: O 162 ASN cc_start: 0.8692 (m-40) cc_final: 0.8490 (m110) REVERT: O 164 LEU cc_start: 0.8113 (tp) cc_final: 0.7822 (tm) REVERT: O 165 GLU cc_start: 0.8127 (tp30) cc_final: 0.7562 (tp30) REVERT: O 166 LYS cc_start: 0.8805 (mttt) cc_final: 0.8267 (mtmm) REVERT: O 208 GLN cc_start: 0.8244 (tm-30) cc_final: 0.7852 (tm-30) REVERT: P 48 MET cc_start: 0.4553 (ppp) cc_final: 0.4097 (ppp) REVERT: P 276 LYS cc_start: 0.6055 (OUTLIER) cc_final: 0.4680 (mtmt) REVERT: g 387 MET cc_start: 0.6659 (tpp) cc_final: 0.6319 (tpp) REVERT: h 426 MET cc_start: 0.3646 (ttm) cc_final: 0.2699 (ttt) REVERT: k 387 MET cc_start: 0.7872 (mmm) cc_final: 0.7085 (tpt) REVERT: k 415 LYS cc_start: 0.7375 (mmmm) cc_final: 0.7007 (mmmm) REVERT: l 348 MET cc_start: 0.4359 (tpp) cc_final: 0.4068 (tpp) REVERT: l 387 MET cc_start: 0.6540 (mtm) cc_final: 0.6286 (mtm) REVERT: l 426 MET cc_start: 0.2214 (ttm) cc_final: 0.1875 (ttm) outliers start: 201 outliers final: 127 residues processed: 1058 average time/residue: 0.7497 time to fit residues: 956.8607 Evaluate side-chains 1129 residues out of total 4576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 983 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 TRP Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 190 LYS Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 207 GLN Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 206 GLU Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 207 GLN Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 80 GLU Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 119 ASN Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 252 VAL Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain F residue 16 HIS Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 187 ILE Chi-restraints excluded: chain F residue 195 THR Chi-restraints excluded: chain F residue 209 ARG Chi-restraints excluded: chain G residue 11 GLU Chi-restraints excluded: chain G residue 17 GLN Chi-restraints excluded: chain G residue 260 ARG Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain H residue 23 HIS Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 116 GLN Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 211 GLN Chi-restraints excluded: chain H residue 252 VAL Chi-restraints excluded: chain H residue 254 LYS Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain H residue 269 VAL Chi-restraints excluded: chain a residue 418 MET Chi-restraints excluded: chain b residue 387 MET Chi-restraints excluded: chain d residue 403 ILE Chi-restraints excluded: chain e residue 360 LYS Chi-restraints excluded: chain f residue 418 MET Chi-restraints excluded: chain I residue 1 TRP Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 133 LYS Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 168 ILE Chi-restraints excluded: chain I residue 190 LYS Chi-restraints excluded: chain I residue 227 ARG Chi-restraints excluded: chain I residue 251 ILE Chi-restraints excluded: chain I residue 253 VAL Chi-restraints excluded: chain I residue 258 THR Chi-restraints excluded: chain J residue 92 LYS Chi-restraints excluded: chain J residue 133 LYS Chi-restraints excluded: chain J residue 137 ILE Chi-restraints excluded: chain J residue 138 GLU Chi-restraints excluded: chain J residue 168 ILE Chi-restraints excluded: chain J residue 207 GLN Chi-restraints excluded: chain J residue 262 LEU Chi-restraints excluded: chain K residue 3 GLU Chi-restraints excluded: chain K residue 104 MET Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 205 LYS Chi-restraints excluded: chain K residue 208 GLN Chi-restraints excluded: chain K residue 241 THR Chi-restraints excluded: chain K residue 252 VAL Chi-restraints excluded: chain K residue 262 LEU Chi-restraints excluded: chain L residue 127 SER Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 137 ILE Chi-restraints excluded: chain L residue 207 GLN Chi-restraints excluded: chain L residue 236 GLU Chi-restraints excluded: chain L residue 253 VAL Chi-restraints excluded: chain L residue 264 ILE Chi-restraints excluded: chain M residue 10 GLU Chi-restraints excluded: chain M residue 17 GLN Chi-restraints excluded: chain M residue 80 GLU Chi-restraints excluded: chain M residue 89 GLU Chi-restraints excluded: chain M residue 119 ASN Chi-restraints excluded: chain M residue 168 ILE Chi-restraints excluded: chain M residue 207 GLN Chi-restraints excluded: chain M residue 210 ILE Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain N residue 16 HIS Chi-restraints excluded: chain N residue 25 GLU Chi-restraints excluded: chain N residue 44 GLN Chi-restraints excluded: chain N residue 65 VAL Chi-restraints excluded: chain N residue 80 GLU Chi-restraints excluded: chain N residue 91 VAL Chi-restraints excluded: chain N residue 133 LYS Chi-restraints excluded: chain N residue 143 ILE Chi-restraints excluded: chain N residue 155 ARG Chi-restraints excluded: chain N residue 168 ILE Chi-restraints excluded: chain N residue 195 THR Chi-restraints excluded: chain N residue 251 ILE Chi-restraints excluded: chain O residue 11 GLU Chi-restraints excluded: chain O residue 17 GLN Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 138 GLU Chi-restraints excluded: chain O residue 187 ILE Chi-restraints excluded: chain O residue 200 ILE Chi-restraints excluded: chain O residue 212 GLN Chi-restraints excluded: chain O residue 251 ILE Chi-restraints excluded: chain O residue 260 ARG Chi-restraints excluded: chain P residue 18 ASP Chi-restraints excluded: chain P residue 80 GLU Chi-restraints excluded: chain P residue 164 LEU Chi-restraints excluded: chain P residue 183 ILE Chi-restraints excluded: chain P residue 185 LEU Chi-restraints excluded: chain P residue 206 GLU Chi-restraints excluded: chain P residue 211 GLN Chi-restraints excluded: chain P residue 252 VAL Chi-restraints excluded: chain P residue 263 VAL Chi-restraints excluded: chain P residue 276 LYS Chi-restraints excluded: chain g residue 396 MET Chi-restraints excluded: chain h residue 387 MET Chi-restraints excluded: chain i residue 426 MET Chi-restraints excluded: chain j residue 359 ILE Chi-restraints excluded: chain k residue 426 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 274 optimal weight: 0.6980 chunk 428 optimal weight: 0.7980 chunk 58 optimal weight: 0.0000 chunk 480 optimal weight: 6.9990 chunk 301 optimal weight: 0.6980 chunk 277 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 311 optimal weight: 0.9990 chunk 241 optimal weight: 0.6980 chunk 89 optimal weight: 6.9990 chunk 84 optimal weight: 5.9990 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 GLN ** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 HIS ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 GLN F 69 HIS F 116 GLN F 266 ASN ** G 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 GLN ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 148 GLN I 150 GLN I 238 GLN J 17 GLN J 129 GLN ** K 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 119 ASN M 213 GLN M 242 GLN ** N 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 69 HIS ** N 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 266 ASN ** O 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 82 ASN ** O 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 393 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.207319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.156138 restraints weight = 64680.679| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 2.42 r_work: 0.3693 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3534 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.227 44538 Z= 0.138 Angle : 0.616 18.855 60392 Z= 0.314 Chirality : 0.042 0.211 6606 Planarity : 0.004 0.062 7462 Dihedral : 13.155 73.626 6360 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.98 % Allowed : 18.59 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.12), residues: 5058 helix: 2.24 (0.10), residues: 2698 sheet: 0.32 (0.17), residues: 920 loop : -1.24 (0.15), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 155 TYR 0.035 0.001 TYR O 134 PHE 0.015 0.001 PHE O 26 TRP 0.018 0.001 TRP I 106 HIS 0.030 0.001 HIS O 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (44474) covalent geometry : angle 0.59527 / 0.31 (60368) hydrogen bonds : bond 0.03803 / 2.58 ( 2434) hydrogen bonds : angle 3.97746 / 2.90 ( 7039) metal coordination : bond 0.05305 / 4.08 ( 64) metal coordination : angle 8.05545 / 6.44 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10116 Ramachandran restraints generated. 5058 Oldfield, 0 Emsley, 5058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10116 Ramachandran restraints generated. 5058 Oldfield, 0 Emsley, 5058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1168 residues out of total 4576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 987 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 GLN cc_start: 0.8517 (tp40) cc_final: 0.8215 (tp-100) REVERT: B 25 GLU cc_start: 0.7542 (tm-30) cc_final: 0.7114 (tm-30) REVERT: B 68 THR cc_start: 0.8528 (t) cc_final: 0.8262 (m) REVERT: B 207 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.8206 (mm-40) REVERT: B 262 LEU cc_start: 0.6992 (OUTLIER) cc_final: 0.6580 (mm) REVERT: C 24 LEU cc_start: 0.8655 (mm) cc_final: 0.8380 (mp) REVERT: C 25 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7198 (tm-30) REVERT: C 34 GLU cc_start: 0.8311 (tp30) cc_final: 0.7702 (tp30) REVERT: C 76 LEU cc_start: 0.7377 (mt) cc_final: 0.7158 (mm) REVERT: C 268 ASP cc_start: 0.7465 (t0) cc_final: 0.6978 (t0) REVERT: D 109 MET cc_start: 0.7172 (mmm) cc_final: 0.6788 (tpp) REVERT: D 188 LYS cc_start: 0.7676 (mmtt) cc_final: 0.7036 (mmtt) REVERT: D 207 GLN cc_start: 0.7302 (OUTLIER) cc_final: 0.6922 (mp10) REVERT: E 1 TRP cc_start: 0.4988 (m-90) cc_final: 0.2861 (m-90) REVERT: E 39 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7861 (mp10) REVERT: E 132 MET cc_start: 0.6699 (tmm) cc_final: 0.6415 (tmm) REVERT: E 137 ILE cc_start: 0.8242 (OUTLIER) cc_final: 0.7935 (tp) REVERT: F 28 ILE cc_start: 0.8529 (pt) cc_final: 0.8041 (mm) REVERT: F 104 MET cc_start: 0.8812 (tpp) cc_final: 0.8601 (mmt) REVERT: F 199 ASP cc_start: 0.7795 (m-30) cc_final: 0.7448 (m-30) REVERT: F 206 GLU cc_start: 0.8279 (tp30) cc_final: 0.7821 (tp30) REVERT: F 209 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.7490 (tmm160) REVERT: G 80 GLU cc_start: 0.7497 (tm-30) cc_final: 0.7009 (tm-30) REVERT: G 82 ASN cc_start: 0.7710 (m110) cc_final: 0.7337 (m110) REVERT: G 104 MET cc_start: 0.8655 (mmm) cc_final: 0.8428 (mmm) REVERT: G 165 GLU cc_start: 0.8314 (tp30) cc_final: 0.7720 (tp30) REVERT: G 208 GLN cc_start: 0.8426 (tm-30) cc_final: 0.8138 (tm-30) REVERT: G 262 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7552 (mm) REVERT: H 10 GLU cc_start: 0.7264 (tp30) cc_final: 0.6916 (tp30) REVERT: H 14 LYS cc_start: 0.8565 (mtmt) cc_final: 0.7727 (mtmt) REVERT: H 34 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7372 (mt-10) REVERT: H 48 MET cc_start: 0.7119 (ppp) cc_final: 0.6902 (ppp) REVERT: H 61 ASP cc_start: 0.7693 (OUTLIER) cc_final: 0.7469 (t70) REVERT: H 76 LEU cc_start: 0.8064 (tp) cc_final: 0.7795 (tm) REVERT: H 79 VAL cc_start: 0.7656 (OUTLIER) cc_final: 0.7292 (p) REVERT: H 82 ASN cc_start: 0.8723 (t0) cc_final: 0.8514 (t0) REVERT: H 185 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7596 (tm) REVERT: H 222 ARG cc_start: 0.6843 (mtp85) cc_final: 0.6594 (mtm180) REVERT: H 254 LYS cc_start: 0.7748 (OUTLIER) cc_final: 0.7512 (ttmm) REVERT: a 387 MET cc_start: 0.7084 (mtm) cc_final: 0.6827 (tpp) REVERT: a 413 MET cc_start: 0.6423 (mtp) cc_final: 0.6076 (mtp) REVERT: b 426 MET cc_start: 0.4599 (ttm) cc_final: 0.4368 (ttp) REVERT: d 348 MET cc_start: 0.7285 (tpp) cc_final: 0.6664 (tpp) REVERT: f 396 MET cc_start: 0.8528 (ttp) cc_final: 0.8105 (ttp) REVERT: f 426 MET cc_start: 0.1907 (mtm) cc_final: 0.0707 (mtm) REVERT: I 133 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8583 (ttmm) REVERT: I 253 VAL cc_start: 0.8455 (OUTLIER) cc_final: 0.8167 (p) REVERT: J 25 GLU cc_start: 0.7508 (tm-30) cc_final: 0.7088 (tm-30) REVERT: J 68 THR cc_start: 0.8522 (t) cc_final: 0.8228 (m) REVERT: J 133 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8390 (mtmt) REVERT: J 207 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.7817 (mp10) REVERT: J 262 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.7134 (mm) REVERT: K 34 GLU cc_start: 0.8451 (tp30) cc_final: 0.8065 (tp30) REVERT: K 262 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7843 (mm) REVERT: K 268 ASP cc_start: 0.7740 (t0) cc_final: 0.7219 (t0) REVERT: L 132 MET cc_start: 0.6527 (ppp) cc_final: 0.6026 (ppp) REVERT: L 188 LYS cc_start: 0.7313 (mmtt) cc_final: 0.6777 (mmtm) REVERT: L 207 GLN cc_start: 0.7306 (OUTLIER) cc_final: 0.6946 (mp10) REVERT: M 1 TRP cc_start: 0.4936 (m-90) cc_final: 0.2698 (m-90) REVERT: M 48 MET cc_start: 0.2522 (tpt) cc_final: 0.1790 (tpt) REVERT: M 70 TYR cc_start: 0.8117 (t80) cc_final: 0.7898 (t80) REVERT: M 107 TYR cc_start: 0.7865 (t80) cc_final: 0.7664 (t80) REVERT: M 264 ILE cc_start: 0.8610 (OUTLIER) cc_final: 0.8401 (mt) REVERT: N 4 ASN cc_start: 0.7404 (p0) cc_final: 0.7054 (p0) REVERT: N 28 ILE cc_start: 0.8312 (pt) cc_final: 0.8078 (mm) REVERT: N 113 LYS cc_start: 0.8668 (mmmt) cc_final: 0.8444 (mmmt) REVERT: N 162 ASN cc_start: 0.8272 (m110) cc_final: 0.8010 (m110) REVERT: N 199 ASP cc_start: 0.7961 (m-30) cc_final: 0.7675 (m-30) REVERT: N 251 ILE cc_start: 0.8350 (OUTLIER) cc_final: 0.8109 (pt) REVERT: O 9 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7539 (mm-30) REVERT: O 164 LEU cc_start: 0.8074 (tp) cc_final: 0.7793 (tm) REVERT: O 165 GLU cc_start: 0.8238 (tp30) cc_final: 0.7687 (tp30) REVERT: O 166 LYS cc_start: 0.8871 (mttt) cc_final: 0.8376 (mtmm) REVERT: O 185 LEU cc_start: 0.8712 (tp) cc_final: 0.8235 (tt) REVERT: O 208 GLN cc_start: 0.8450 (tm-30) cc_final: 0.8064 (tm-30) REVERT: P 36 ILE cc_start: 0.8202 (mm) cc_final: 0.7746 (tt) REVERT: P 48 MET cc_start: 0.4664 (ppp) cc_final: 0.4183 (ppp) REVERT: P 178 LEU cc_start: 0.8349 (tm) cc_final: 0.8057 (tp) REVERT: P 276 LYS cc_start: 0.6134 (OUTLIER) cc_final: 0.4623 (mtmt) REVERT: g 387 MET cc_start: 0.6764 (tpp) cc_final: 0.6417 (tpp) REVERT: h 426 MET cc_start: 0.3910 (ttm) cc_final: 0.2971 (ttt) REVERT: j 356 HIS cc_start: 0.7422 (t-170) cc_final: 0.7035 (t-170) REVERT: k 387 MET cc_start: 0.7854 (mmm) cc_final: 0.7047 (tpt) REVERT: l 348 MET cc_start: 0.4364 (tpp) cc_final: 0.4065 (tpp) REVERT: l 387 MET cc_start: 0.6527 (mtm) cc_final: 0.6272 (mtm) REVERT: l 426 MET cc_start: 0.2253 (ttm) cc_final: 0.1869 (ttm) outliers start: 181 outliers final: 121 residues processed: 1054 average time/residue: 0.5369 time to fit residues: 684.0401 Evaluate side-chains 1119 residues out of total 4576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 976 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 TRP Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 190 LYS Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 207 GLN Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 207 GLN Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 80 GLU Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain F residue 16 HIS Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 187 ILE Chi-restraints excluded: chain F residue 195 THR Chi-restraints excluded: chain F residue 209 ARG Chi-restraints excluded: chain G residue 11 GLU Chi-restraints excluded: chain G residue 17 GLN Chi-restraints excluded: chain G residue 86 ILE Chi-restraints excluded: chain G residue 260 ARG Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain H residue 23 HIS Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 116 GLN Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 154 GLU Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 211 GLN Chi-restraints excluded: chain H residue 252 VAL Chi-restraints excluded: chain H residue 254 LYS Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain a residue 418 MET Chi-restraints excluded: chain c residue 378 ASP Chi-restraints excluded: chain d residue 369 ASP Chi-restraints excluded: chain f residue 418 MET Chi-restraints excluded: chain I residue 1 TRP Chi-restraints excluded: chain I residue 133 LYS Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 168 ILE Chi-restraints excluded: chain I residue 190 LYS Chi-restraints excluded: chain I residue 227 ARG Chi-restraints excluded: chain I residue 251 ILE Chi-restraints excluded: chain I residue 253 VAL Chi-restraints excluded: chain I residue 258 THR Chi-restraints excluded: chain J residue 92 LYS Chi-restraints excluded: chain J residue 133 LYS Chi-restraints excluded: chain J residue 137 ILE Chi-restraints excluded: chain J residue 138 GLU Chi-restraints excluded: chain J residue 168 ILE Chi-restraints excluded: chain J residue 207 GLN Chi-restraints excluded: chain J residue 262 LEU Chi-restraints excluded: chain K residue 104 MET Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 205 LYS Chi-restraints excluded: chain K residue 208 GLN Chi-restraints excluded: chain K residue 241 THR Chi-restraints excluded: chain K residue 252 VAL Chi-restraints excluded: chain K residue 262 LEU Chi-restraints excluded: chain L residue 127 SER Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 137 ILE Chi-restraints excluded: chain L residue 207 GLN Chi-restraints excluded: chain L residue 236 GLU Chi-restraints excluded: chain L residue 253 VAL Chi-restraints excluded: chain L residue 264 ILE Chi-restraints excluded: chain M residue 10 GLU Chi-restraints excluded: chain M residue 17 GLN Chi-restraints excluded: chain M residue 80 GLU Chi-restraints excluded: chain M residue 85 LEU Chi-restraints excluded: chain M residue 89 GLU Chi-restraints excluded: chain M residue 119 ASN Chi-restraints excluded: chain M residue 168 ILE Chi-restraints excluded: chain M residue 207 GLN Chi-restraints excluded: chain M residue 210 ILE Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 264 ILE Chi-restraints excluded: chain M residue 276 LYS Chi-restraints excluded: chain N residue 16 HIS Chi-restraints excluded: chain N residue 25 GLU Chi-restraints excluded: chain N residue 44 GLN Chi-restraints excluded: chain N residue 65 VAL Chi-restraints excluded: chain N residue 91 VAL Chi-restraints excluded: chain N residue 133 LYS Chi-restraints excluded: chain N residue 143 ILE Chi-restraints excluded: chain N residue 155 ARG Chi-restraints excluded: chain N residue 168 ILE Chi-restraints excluded: chain N residue 195 THR Chi-restraints excluded: chain N residue 213 GLN Chi-restraints excluded: chain N residue 251 ILE Chi-restraints excluded: chain O residue 11 GLU Chi-restraints excluded: chain O residue 17 GLN Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 138 GLU Chi-restraints excluded: chain O residue 200 ILE Chi-restraints excluded: chain O residue 212 GLN Chi-restraints excluded: chain O residue 225 TYR Chi-restraints excluded: chain O residue 260 ARG Chi-restraints excluded: chain P residue 10 GLU Chi-restraints excluded: chain P residue 18 ASP Chi-restraints excluded: chain P residue 80 GLU Chi-restraints excluded: chain P residue 164 LEU Chi-restraints excluded: chain P residue 183 ILE Chi-restraints excluded: chain P residue 185 LEU Chi-restraints excluded: chain P residue 206 GLU Chi-restraints excluded: chain P residue 243 VAL Chi-restraints excluded: chain P residue 263 VAL Chi-restraints excluded: chain P residue 276 LYS Chi-restraints excluded: chain h residue 387 MET Chi-restraints excluded: chain i residue 426 MET Chi-restraints excluded: chain j residue 359 ILE Chi-restraints excluded: chain k residue 419 LEU Chi-restraints excluded: chain l residue 418 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 246 optimal weight: 0.9990 chunk 179 optimal weight: 9.9990 chunk 284 optimal weight: 3.9990 chunk 219 optimal weight: 0.0040 chunk 193 optimal weight: 3.9990 chunk 411 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 491 optimal weight: 7.9990 chunk 27 optimal weight: 0.9990 chunk 137 optimal weight: 0.9980 chunk 187 optimal weight: 0.3980 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 GLN ** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 242 GLN ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 HIS F 172 ASN F 266 ASN ** G 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 356 HIS I 148 GLN I 150 GLN J 17 GLN J 129 GLN ** K 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 238 GLN ** L 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 213 GLN M 242 GLN ** N 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 69 HIS ** N 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 266 ASN ** O 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 82 ASN ** O 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 162 ASN ** O 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.206880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.157361 restraints weight = 64225.998| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 2.82 r_work: 0.3667 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.255 44538 Z= 0.149 Angle : 0.635 22.034 60392 Z= 0.322 Chirality : 0.043 0.206 6606 Planarity : 0.004 0.062 7462 Dihedral : 13.160 73.473 6360 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.94 % Allowed : 19.03 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.12), residues: 5058 helix: 2.19 (0.10), residues: 2706 sheet: 0.37 (0.17), residues: 908 loop : -1.27 (0.15), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG j 351 TYR 0.024 0.001 TYR O 70 PHE 0.018 0.001 PHE O 26 TRP 0.017 0.001 TRP A 106 HIS 0.029 0.002 HIS O 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (44474) covalent geometry : angle 0.61072 / 0.32 (60368) hydrogen bonds : bond 0.03908 / 2.65 ( 2434) hydrogen bonds : angle 3.99098 / 2.91 ( 7039) metal coordination : bond 0.05679 / 4.41 ( 64) metal coordination : angle 8.67489 / 7.00 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10116 Ramachandran restraints generated. 5058 Oldfield, 0 Emsley, 5058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10116 Ramachandran restraints generated. 5058 Oldfield, 0 Emsley, 5058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1156 residues out of total 4576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 977 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 GLN cc_start: 0.8322 (tp40) cc_final: 0.8050 (tp-100) REVERT: B 25 GLU cc_start: 0.7403 (tm-30) cc_final: 0.6967 (tm-30) REVERT: B 68 THR cc_start: 0.8428 (t) cc_final: 0.8165 (m) REVERT: B 207 GLN cc_start: 0.8166 (OUTLIER) cc_final: 0.7957 (mm-40) REVERT: B 262 LEU cc_start: 0.6956 (OUTLIER) cc_final: 0.6550 (mm) REVERT: C 25 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.6969 (tm-30) REVERT: C 34 GLU cc_start: 0.8063 (tp30) cc_final: 0.7401 (tp30) REVERT: C 76 LEU cc_start: 0.7257 (mt) cc_final: 0.7036 (mm) REVERT: C 268 ASP cc_start: 0.7293 (t0) cc_final: 0.6787 (t0) REVERT: D 109 MET cc_start: 0.7007 (mmm) cc_final: 0.6638 (tpp) REVERT: D 188 LYS cc_start: 0.7466 (mmtt) cc_final: 0.6795 (mmtt) REVERT: D 207 GLN cc_start: 0.7332 (OUTLIER) cc_final: 0.6931 (mp10) REVERT: E 1 TRP cc_start: 0.4714 (m-90) cc_final: 0.2620 (m-90) REVERT: E 132 MET cc_start: 0.6312 (tmm) cc_final: 0.5991 (tmm) REVERT: E 137 ILE cc_start: 0.8144 (OUTLIER) cc_final: 0.7846 (tp) REVERT: F 28 ILE cc_start: 0.8495 (pt) cc_final: 0.8035 (mm) REVERT: F 104 MET cc_start: 0.8710 (tpp) cc_final: 0.8483 (mmt) REVERT: F 199 ASP cc_start: 0.7482 (m-30) cc_final: 0.7123 (m-30) REVERT: F 206 GLU cc_start: 0.7984 (tp30) cc_final: 0.7470 (tp30) REVERT: F 209 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.7327 (tmm160) REVERT: G 80 GLU cc_start: 0.7256 (tm-30) cc_final: 0.6791 (tm-30) REVERT: G 82 ASN cc_start: 0.7564 (m110) cc_final: 0.7148 (m110) REVERT: G 104 MET cc_start: 0.8360 (mmm) cc_final: 0.8109 (mmm) REVERT: G 137 ILE cc_start: 0.8741 (mt) cc_final: 0.8502 (mt) REVERT: G 165 GLU cc_start: 0.8181 (tp30) cc_final: 0.7572 (tp30) REVERT: G 208 GLN cc_start: 0.8266 (tm-30) cc_final: 0.7978 (tm-30) REVERT: G 262 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7573 (mm) REVERT: H 10 GLU cc_start: 0.7213 (tp30) cc_final: 0.6916 (tp30) REVERT: H 14 LYS cc_start: 0.8545 (mtmt) cc_final: 0.8291 (mttm) REVERT: H 34 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7291 (mt-10) REVERT: H 48 MET cc_start: 0.7190 (ppp) cc_final: 0.6950 (ppp) REVERT: H 61 ASP cc_start: 0.7465 (OUTLIER) cc_final: 0.7234 (t70) REVERT: H 76 LEU cc_start: 0.7932 (tp) cc_final: 0.7658 (tm) REVERT: H 79 VAL cc_start: 0.7603 (OUTLIER) cc_final: 0.7236 (p) REVERT: H 82 ASN cc_start: 0.8611 (t0) cc_final: 0.8358 (t0) REVERT: H 185 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7461 (tm) REVERT: H 254 LYS cc_start: 0.7660 (OUTLIER) cc_final: 0.7436 (ttmm) REVERT: a 387 MET cc_start: 0.7066 (mtm) cc_final: 0.6801 (tpp) REVERT: a 413 MET cc_start: 0.6361 (mtp) cc_final: 0.6014 (mtp) REVERT: b 426 MET cc_start: 0.4351 (ttm) cc_final: 0.4122 (ttp) REVERT: d 348 MET cc_start: 0.7173 (tpp) cc_final: 0.6562 (tpp) REVERT: f 396 MET cc_start: 0.8512 (ttp) cc_final: 0.8082 (ttp) REVERT: f 426 MET cc_start: 0.1874 (mtm) cc_final: 0.0955 (mtm) REVERT: I 253 VAL cc_start: 0.8277 (OUTLIER) cc_final: 0.7994 (p) REVERT: J 25 GLU cc_start: 0.7373 (tm-30) cc_final: 0.6955 (tm-30) REVERT: J 68 THR cc_start: 0.8439 (t) cc_final: 0.8149 (m) REVERT: J 109 MET cc_start: 0.7584 (mmp) cc_final: 0.7229 (mmp) REVERT: J 133 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.8287 (mtmt) REVERT: J 207 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.7464 (mp10) REVERT: J 262 LEU cc_start: 0.7369 (OUTLIER) cc_final: 0.7039 (mm) REVERT: K 25 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7114 (tm-30) REVERT: K 34 GLU cc_start: 0.8139 (tp30) cc_final: 0.7718 (tp30) REVERT: K 262 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7658 (mm) REVERT: K 268 ASP cc_start: 0.7592 (t0) cc_final: 0.7042 (t0) REVERT: L 18 ASP cc_start: 0.6749 (p0) cc_final: 0.6466 (p0) REVERT: L 132 MET cc_start: 0.6193 (ppp) cc_final: 0.5753 (ppp) REVERT: L 188 LYS cc_start: 0.7104 (mmtt) cc_final: 0.6560 (mmtm) REVERT: L 207 GLN cc_start: 0.7303 (OUTLIER) cc_final: 0.6909 (mp10) REVERT: M 1 TRP cc_start: 0.4722 (m-90) cc_final: 0.2555 (m-90) REVERT: M 48 MET cc_start: 0.2682 (tpt) cc_final: 0.1854 (tpt) REVERT: M 107 TYR cc_start: 0.7834 (t80) cc_final: 0.7629 (t80) REVERT: M 264 ILE cc_start: 0.8483 (OUTLIER) cc_final: 0.8269 (mt) REVERT: N 4 ASN cc_start: 0.7367 (p0) cc_final: 0.6974 (p0) REVERT: N 28 ILE cc_start: 0.8296 (pt) cc_final: 0.8009 (mm) REVERT: N 113 LYS cc_start: 0.8510 (mmmt) cc_final: 0.8278 (mmmt) REVERT: N 162 ASN cc_start: 0.8081 (m110) cc_final: 0.7802 (m110) REVERT: N 199 ASP cc_start: 0.7619 (m-30) cc_final: 0.7345 (m-30) REVERT: O 9 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7301 (mm-30) REVERT: O 164 LEU cc_start: 0.8095 (tp) cc_final: 0.7792 (tm) REVERT: O 165 GLU cc_start: 0.8101 (tp30) cc_final: 0.7508 (tp30) REVERT: O 166 LYS cc_start: 0.8742 (mttt) cc_final: 0.8279 (mtmm) REVERT: O 185 LEU cc_start: 0.8589 (tp) cc_final: 0.8064 (tt) REVERT: O 208 GLN cc_start: 0.8254 (tm-30) cc_final: 0.7871 (tm-30) REVERT: P 14 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8404 (mtmt) REVERT: P 36 ILE cc_start: 0.8221 (mm) cc_final: 0.7818 (tt) REVERT: P 48 MET cc_start: 0.4630 (ppp) cc_final: 0.4155 (ppp) REVERT: P 178 LEU cc_start: 0.8299 (tm) cc_final: 0.8010 (tp) REVERT: P 276 LYS cc_start: 0.5887 (OUTLIER) cc_final: 0.4511 (mtmt) REVERT: g 387 MET cc_start: 0.6723 (tpp) cc_final: 0.6381 (tpp) REVERT: h 426 MET cc_start: 0.3721 (ttm) cc_final: 0.2811 (ttt) REVERT: k 387 MET cc_start: 0.7847 (mmm) cc_final: 0.7060 (tpt) REVERT: l 348 MET cc_start: 0.4345 (tpp) cc_final: 0.4062 (tpp) REVERT: l 387 MET cc_start: 0.6536 (mtm) cc_final: 0.6291 (mtm) REVERT: l 426 MET cc_start: 0.2175 (ttm) cc_final: 0.1802 (ttm) outliers start: 179 outliers final: 129 residues processed: 1039 average time/residue: 0.5190 time to fit residues: 651.9508 Evaluate side-chains 1122 residues out of total 4576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 972 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 TRP Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 190 LYS Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 207 GLN Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 207 GLN Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 80 GLU Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 119 ASN Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain F residue 16 HIS Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 34 GLU Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 187 ILE Chi-restraints excluded: chain F residue 195 THR Chi-restraints excluded: chain F residue 209 ARG Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 11 GLU Chi-restraints excluded: chain G residue 17 GLN Chi-restraints excluded: chain G residue 260 ARG Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain H residue 23 HIS Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 109 MET Chi-restraints excluded: chain H residue 116 GLN Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 154 GLU Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 211 GLN Chi-restraints excluded: chain H residue 252 VAL Chi-restraints excluded: chain H residue 254 LYS Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain a residue 418 MET Chi-restraints excluded: chain d residue 359 ILE Chi-restraints excluded: chain d residue 369 ASP Chi-restraints excluded: chain e residue 360 LYS Chi-restraints excluded: chain f residue 418 MET Chi-restraints excluded: chain I residue 1 TRP Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 152 LEU Chi-restraints excluded: chain I residue 168 ILE Chi-restraints excluded: chain I residue 190 LYS Chi-restraints excluded: chain I residue 227 ARG Chi-restraints excluded: chain I residue 251 ILE Chi-restraints excluded: chain I residue 253 VAL Chi-restraints excluded: chain I residue 258 THR Chi-restraints excluded: chain J residue 92 LYS Chi-restraints excluded: chain J residue 133 LYS Chi-restraints excluded: chain J residue 137 ILE Chi-restraints excluded: chain J residue 138 GLU Chi-restraints excluded: chain J residue 168 ILE Chi-restraints excluded: chain J residue 207 GLN Chi-restraints excluded: chain J residue 262 LEU Chi-restraints excluded: chain K residue 25 GLU Chi-restraints excluded: chain K residue 104 MET Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 205 LYS Chi-restraints excluded: chain K residue 208 GLN Chi-restraints excluded: chain K residue 238 GLN Chi-restraints excluded: chain K residue 241 THR Chi-restraints excluded: chain K residue 252 VAL Chi-restraints excluded: chain K residue 262 LEU Chi-restraints excluded: chain L residue 127 SER Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 137 ILE Chi-restraints excluded: chain L residue 207 GLN Chi-restraints excluded: chain L residue 236 GLU Chi-restraints excluded: chain L residue 253 VAL Chi-restraints excluded: chain L residue 264 ILE Chi-restraints excluded: chain M residue 10 GLU Chi-restraints excluded: chain M residue 17 GLN Chi-restraints excluded: chain M residue 80 GLU Chi-restraints excluded: chain M residue 85 LEU Chi-restraints excluded: chain M residue 89 GLU Chi-restraints excluded: chain M residue 119 ASN Chi-restraints excluded: chain M residue 168 ILE Chi-restraints excluded: chain M residue 207 GLN Chi-restraints excluded: chain M residue 210 ILE Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 264 ILE Chi-restraints excluded: chain M residue 272 ILE Chi-restraints excluded: chain M residue 276 LYS Chi-restraints excluded: chain N residue 16 HIS Chi-restraints excluded: chain N residue 25 GLU Chi-restraints excluded: chain N residue 44 GLN Chi-restraints excluded: chain N residue 65 VAL Chi-restraints excluded: chain N residue 91 VAL Chi-restraints excluded: chain N residue 133 LYS Chi-restraints excluded: chain N residue 143 ILE Chi-restraints excluded: chain N residue 155 ARG Chi-restraints excluded: chain N residue 168 ILE Chi-restraints excluded: chain N residue 195 THR Chi-restraints excluded: chain N residue 251 ILE Chi-restraints excluded: chain O residue 11 GLU Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 138 GLU Chi-restraints excluded: chain O residue 200 ILE Chi-restraints excluded: chain O residue 212 GLN Chi-restraints excluded: chain O residue 225 TYR Chi-restraints excluded: chain O residue 251 ILE Chi-restraints excluded: chain O residue 260 ARG Chi-restraints excluded: chain O residue 264 ILE Chi-restraints excluded: chain P residue 10 GLU Chi-restraints excluded: chain P residue 14 LYS Chi-restraints excluded: chain P residue 18 ASP Chi-restraints excluded: chain P residue 80 GLU Chi-restraints excluded: chain P residue 164 LEU Chi-restraints excluded: chain P residue 183 ILE Chi-restraints excluded: chain P residue 185 LEU Chi-restraints excluded: chain P residue 206 GLU Chi-restraints excluded: chain P residue 243 VAL Chi-restraints excluded: chain P residue 263 VAL Chi-restraints excluded: chain P residue 276 LYS Chi-restraints excluded: chain h residue 387 MET Chi-restraints excluded: chain i residue 426 MET Chi-restraints excluded: chain j residue 359 ILE Chi-restraints excluded: chain k residue 419 LEU Chi-restraints excluded: chain l residue 418 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 217 optimal weight: 5.9990 chunk 271 optimal weight: 0.9980 chunk 306 optimal weight: 6.9990 chunk 480 optimal weight: 7.9990 chunk 166 optimal weight: 1.9990 chunk 362 optimal weight: 0.8980 chunk 14 optimal weight: 0.0010 chunk 295 optimal weight: 0.4980 chunk 507 optimal weight: 8.9990 chunk 126 optimal weight: 0.7980 chunk 357 optimal weight: 0.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 GLN A 207 GLN ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 207 GLN ** E 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 242 GLN ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 HIS F 266 ASN ** G 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 356 HIS I 148 GLN I 150 GLN I 238 GLN J 17 GLN J 129 GLN ** K 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 238 GLN ** L 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 119 ASN M 242 GLN ** N 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 266 ASN ** O 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 17 GLN ** O 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 82 ASN ** O 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.206718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.156573 restraints weight = 64477.511| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 2.83 r_work: 0.3666 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.270 44538 Z= 0.148 Angle : 0.645 23.129 60392 Z= 0.328 Chirality : 0.042 0.202 6606 Planarity : 0.004 0.061 7462 Dihedral : 13.156 73.196 6360 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.74 % Allowed : 19.51 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.12), residues: 5058 helix: 2.17 (0.10), residues: 2706 sheet: 0.33 (0.17), residues: 920 loop : -1.26 (0.15), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG L 155 TYR 0.024 0.001 TYR O 70 PHE 0.017 0.001 PHE O 26 TRP 0.031 0.001 TRP A 237 HIS 0.027 0.002 HIS O 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (44474) covalent geometry : angle 0.61955 / 0.33 (60368) hydrogen bonds : bond 0.03862 / 2.62 ( 2434) hydrogen bonds : angle 4.00685 / 2.92 ( 7039) metal coordination : bond 0.05849 / 4.59 ( 64) metal coordination : angle 8.93545 / 7.19 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10116 Ramachandran restraints generated. 5058 Oldfield, 0 Emsley, 5058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10116 Ramachandran restraints generated. 5058 Oldfield, 0 Emsley, 5058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1159 residues out of total 4576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 989 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 GLU cc_start: 0.7961 (tp30) cc_final: 0.7748 (tp30) REVERT: B 25 GLU cc_start: 0.7399 (tm-30) cc_final: 0.6959 (tm-30) REVERT: B 68 THR cc_start: 0.8425 (t) cc_final: 0.8162 (m) REVERT: B 207 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7975 (mm-40) REVERT: B 262 LEU cc_start: 0.6955 (OUTLIER) cc_final: 0.6550 (mm) REVERT: C 25 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7032 (tm-30) REVERT: C 34 GLU cc_start: 0.8066 (tp30) cc_final: 0.7411 (tp30) REVERT: C 76 LEU cc_start: 0.7241 (mt) cc_final: 0.7021 (mm) REVERT: C 268 ASP cc_start: 0.7307 (t0) cc_final: 0.6816 (t0) REVERT: D 109 MET cc_start: 0.7025 (mmm) cc_final: 0.6648 (tpp) REVERT: D 188 LYS cc_start: 0.7483 (mmtt) cc_final: 0.6783 (mmtt) REVERT: D 207 GLN cc_start: 0.7028 (OUTLIER) cc_final: 0.6672 (mp-120) REVERT: E 1 TRP cc_start: 0.4733 (m-90) cc_final: 0.2632 (m-90) REVERT: E 132 MET cc_start: 0.6330 (tmm) cc_final: 0.6007 (tmm) REVERT: E 137 ILE cc_start: 0.8158 (OUTLIER) cc_final: 0.7868 (tp) REVERT: F 28 ILE cc_start: 0.8482 (pt) cc_final: 0.8039 (mm) REVERT: F 104 MET cc_start: 0.8725 (tpp) cc_final: 0.8499 (mmt) REVERT: F 199 ASP cc_start: 0.7485 (m-30) cc_final: 0.7109 (m-30) REVERT: F 206 GLU cc_start: 0.7998 (tp30) cc_final: 0.7483 (tp30) REVERT: F 209 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.7328 (tmm160) REVERT: G 79 VAL cc_start: 0.8096 (t) cc_final: 0.7784 (p) REVERT: G 80 GLU cc_start: 0.7228 (tm-30) cc_final: 0.6738 (tm-30) REVERT: G 82 ASN cc_start: 0.7657 (m110) cc_final: 0.7213 (m110) REVERT: G 104 MET cc_start: 0.8369 (mmm) cc_final: 0.8130 (mmm) REVERT: G 137 ILE cc_start: 0.8760 (mt) cc_final: 0.8520 (mt) REVERT: G 165 GLU cc_start: 0.8185 (tp30) cc_final: 0.7547 (tp30) REVERT: G 208 GLN cc_start: 0.8280 (tm-30) cc_final: 0.7976 (tm-30) REVERT: G 262 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7573 (mm) REVERT: H 10 GLU cc_start: 0.7308 (tp30) cc_final: 0.6906 (tp30) REVERT: H 14 LYS cc_start: 0.8546 (mtmt) cc_final: 0.8099 (mtpp) REVERT: H 34 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7304 (mt-10) REVERT: H 48 MET cc_start: 0.7176 (ppp) cc_final: 0.6943 (ppp) REVERT: H 61 ASP cc_start: 0.7481 (OUTLIER) cc_final: 0.7232 (t70) REVERT: H 76 LEU cc_start: 0.7934 (tp) cc_final: 0.7663 (tm) REVERT: H 79 VAL cc_start: 0.7640 (OUTLIER) cc_final: 0.7231 (p) REVERT: H 185 LEU cc_start: 0.7730 (OUTLIER) cc_final: 0.7466 (tm) REVERT: H 254 LYS cc_start: 0.7655 (OUTLIER) cc_final: 0.7436 (ttmm) REVERT: a 387 MET cc_start: 0.7097 (mtm) cc_final: 0.6829 (tpp) REVERT: a 413 MET cc_start: 0.6397 (mtp) cc_final: 0.6042 (mtp) REVERT: b 348 MET cc_start: 0.4289 (ppp) cc_final: 0.2428 (ttp) REVERT: b 426 MET cc_start: 0.4426 (ttm) cc_final: 0.4203 (ttp) REVERT: d 348 MET cc_start: 0.7145 (tpp) cc_final: 0.6516 (tpp) REVERT: d 386 THR cc_start: 0.8586 (p) cc_final: 0.8366 (t) REVERT: f 396 MET cc_start: 0.8522 (ttp) cc_final: 0.8093 (ttp) REVERT: f 426 MET cc_start: 0.1862 (mtm) cc_final: 0.1047 (mtm) REVERT: I 168 ILE cc_start: 0.8794 (OUTLIER) cc_final: 0.8334 (mp) REVERT: I 238 GLN cc_start: 0.7255 (mm-40) cc_final: 0.6808 (mp-120) REVERT: I 253 VAL cc_start: 0.8268 (OUTLIER) cc_final: 0.7979 (p) REVERT: J 25 GLU cc_start: 0.7373 (tm-30) cc_final: 0.6957 (tm-30) REVERT: J 68 THR cc_start: 0.8431 (t) cc_final: 0.8144 (m) REVERT: J 133 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.8280 (mtmt) REVERT: J 207 GLN cc_start: 0.8095 (OUTLIER) cc_final: 0.7467 (mp10) REVERT: J 262 LEU cc_start: 0.7367 (OUTLIER) cc_final: 0.7037 (mm) REVERT: K 25 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7093 (tm-30) REVERT: K 34 GLU cc_start: 0.8153 (tp30) cc_final: 0.7735 (tp30) REVERT: K 92 LYS cc_start: 0.7887 (mmtm) cc_final: 0.7608 (mmtm) REVERT: K 262 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7656 (mm) REVERT: K 268 ASP cc_start: 0.7606 (t0) cc_final: 0.7052 (t0) REVERT: L 18 ASP cc_start: 0.6751 (p0) cc_final: 0.6471 (p0) REVERT: L 132 MET cc_start: 0.6213 (ppp) cc_final: 0.5774 (ppp) REVERT: L 166 LYS cc_start: 0.8215 (ptmt) cc_final: 0.7798 (pttt) REVERT: L 188 LYS cc_start: 0.7109 (mmtt) cc_final: 0.6568 (mmtm) REVERT: L 207 GLN cc_start: 0.7309 (OUTLIER) cc_final: 0.6941 (mp10) REVERT: M 1 TRP cc_start: 0.4715 (m-90) cc_final: 0.2552 (m-90) REVERT: M 48 MET cc_start: 0.2687 (tpt) cc_final: 0.1856 (tpt) REVERT: M 264 ILE cc_start: 0.8484 (OUTLIER) cc_final: 0.8275 (mt) REVERT: N 4 ASN cc_start: 0.7370 (p0) cc_final: 0.6982 (p0) REVERT: N 28 ILE cc_start: 0.8289 (pt) cc_final: 0.8004 (mm) REVERT: N 45 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8129 (mt-10) REVERT: N 113 LYS cc_start: 0.8515 (mmmt) cc_final: 0.8280 (mmmt) REVERT: N 162 ASN cc_start: 0.8082 (m110) cc_final: 0.7800 (m110) REVERT: N 199 ASP cc_start: 0.7666 (m-30) cc_final: 0.7380 (m-30) REVERT: N 251 ILE cc_start: 0.8256 (OUTLIER) cc_final: 0.8046 (pt) REVERT: O 9 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7298 (mm-30) REVERT: O 162 ASN cc_start: 0.8649 (m110) cc_final: 0.8374 (m110) REVERT: O 164 LEU cc_start: 0.8054 (tp) cc_final: 0.7761 (tm) REVERT: O 165 GLU cc_start: 0.8106 (tp30) cc_final: 0.7511 (tp30) REVERT: O 166 LYS cc_start: 0.8754 (mttt) cc_final: 0.8304 (mtmm) REVERT: O 185 LEU cc_start: 0.8593 (tp) cc_final: 0.8061 (tt) REVERT: O 208 GLN cc_start: 0.8265 (tm-30) cc_final: 0.7877 (tm-30) REVERT: P 14 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8419 (mtmt) REVERT: P 36 ILE cc_start: 0.8211 (mm) cc_final: 0.7813 (tt) REVERT: P 48 MET cc_start: 0.4694 (ppp) cc_final: 0.4212 (ppp) REVERT: P 178 LEU cc_start: 0.8301 (tm) cc_final: 0.8008 (tp) REVERT: P 276 LYS cc_start: 0.5894 (OUTLIER) cc_final: 0.4509 (mtmt) REVERT: g 387 MET cc_start: 0.6717 (tpp) cc_final: 0.6384 (tpp) REVERT: h 426 MET cc_start: 0.3757 (ttm) cc_final: 0.2885 (ttt) REVERT: k 387 MET cc_start: 0.7815 (mmm) cc_final: 0.7031 (tpt) REVERT: l 348 MET cc_start: 0.4266 (tpp) cc_final: 0.3976 (tpp) REVERT: l 387 MET cc_start: 0.6534 (mtm) cc_final: 0.6292 (mtm) REVERT: l 426 MET cc_start: 0.2213 (ttm) cc_final: 0.1838 (ttm) outliers start: 170 outliers final: 130 residues processed: 1050 average time/residue: 0.4951 time to fit residues: 630.1711 Evaluate side-chains 1130 residues out of total 4576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 977 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 TRP Chi-restraints excluded: chain A residue 7 LEU Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 133 LYS Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 190 LYS Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain B residue 92 LYS Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 207 GLN Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain C residue 3 GLU Chi-restraints excluded: chain C residue 25 GLU Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 207 GLN Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 80 GLU Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 119 ASN Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 165 GLU Chi-restraints excluded: chain E residue 168 ILE Chi-restraints excluded: chain E residue 207 GLN Chi-restraints excluded: chain E residue 210 ILE Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain F residue 16 HIS Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 34 GLU Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 155 ARG Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 187 ILE Chi-restraints excluded: chain F residue 195 THR Chi-restraints excluded: chain F residue 209 ARG Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 11 GLU Chi-restraints excluded: chain G residue 17 GLN Chi-restraints excluded: chain G residue 260 ARG Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain H residue 23 HIS Chi-restraints excluded: chain H residue 61 ASP Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 109 MET Chi-restraints excluded: chain H residue 116 GLN Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain H residue 154 GLU Chi-restraints excluded: chain H residue 164 LEU Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 211 GLN Chi-restraints excluded: chain H residue 252 VAL Chi-restraints excluded: chain H residue 254 LYS Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain a residue 418 MET Chi-restraints excluded: chain d residue 359 ILE Chi-restraints excluded: chain e residue 360 LYS Chi-restraints excluded: chain f residue 418 MET Chi-restraints excluded: chain I residue 1 TRP Chi-restraints excluded: chain I residue 7 LEU Chi-restraints excluded: chain I residue 133 LYS Chi-restraints excluded: chain I residue 141 THR Chi-restraints excluded: chain I residue 152 LEU Chi-restraints excluded: chain I residue 168 ILE Chi-restraints excluded: chain I residue 190 LYS Chi-restraints excluded: chain I residue 251 ILE Chi-restraints excluded: chain I residue 253 VAL Chi-restraints excluded: chain I residue 258 THR Chi-restraints excluded: chain J residue 92 LYS Chi-restraints excluded: chain J residue 98 GLU Chi-restraints excluded: chain J residue 133 LYS Chi-restraints excluded: chain J residue 137 ILE Chi-restraints excluded: chain J residue 138 GLU Chi-restraints excluded: chain J residue 168 ILE Chi-restraints excluded: chain J residue 207 GLN Chi-restraints excluded: chain J residue 262 LEU Chi-restraints excluded: chain K residue 25 GLU Chi-restraints excluded: chain K residue 104 MET Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 205 LYS Chi-restraints excluded: chain K residue 208 GLN Chi-restraints excluded: chain K residue 238 GLN Chi-restraints excluded: chain K residue 241 THR Chi-restraints excluded: chain K residue 252 VAL Chi-restraints excluded: chain K residue 262 LEU Chi-restraints excluded: chain L residue 127 SER Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 137 ILE Chi-restraints excluded: chain L residue 207 GLN Chi-restraints excluded: chain L residue 236 GLU Chi-restraints excluded: chain L residue 253 VAL Chi-restraints excluded: chain L residue 264 ILE Chi-restraints excluded: chain M residue 10 GLU Chi-restraints excluded: chain M residue 17 GLN Chi-restraints excluded: chain M residue 80 GLU Chi-restraints excluded: chain M residue 85 LEU Chi-restraints excluded: chain M residue 89 GLU Chi-restraints excluded: chain M residue 168 ILE Chi-restraints excluded: chain M residue 207 GLN Chi-restraints excluded: chain M residue 210 ILE Chi-restraints excluded: chain M residue 252 VAL Chi-restraints excluded: chain M residue 262 LEU Chi-restraints excluded: chain M residue 264 ILE Chi-restraints excluded: chain M residue 272 ILE Chi-restraints excluded: chain M residue 276 LYS Chi-restraints excluded: chain N residue 16 HIS Chi-restraints excluded: chain N residue 25 GLU Chi-restraints excluded: chain N residue 44 GLN Chi-restraints excluded: chain N residue 65 VAL Chi-restraints excluded: chain N residue 91 VAL Chi-restraints excluded: chain N residue 133 LYS Chi-restraints excluded: chain N residue 143 ILE Chi-restraints excluded: chain N residue 155 ARG Chi-restraints excluded: chain N residue 161 LYS Chi-restraints excluded: chain N residue 168 ILE Chi-restraints excluded: chain N residue 195 THR Chi-restraints excluded: chain N residue 251 ILE Chi-restraints excluded: chain O residue 11 GLU Chi-restraints excluded: chain O residue 20 VAL Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 138 GLU Chi-restraints excluded: chain O residue 212 GLN Chi-restraints excluded: chain O residue 225 TYR Chi-restraints excluded: chain O residue 251 ILE Chi-restraints excluded: chain O residue 260 ARG Chi-restraints excluded: chain O residue 264 ILE Chi-restraints excluded: chain P residue 14 LYS Chi-restraints excluded: chain P residue 18 ASP Chi-restraints excluded: chain P residue 80 GLU Chi-restraints excluded: chain P residue 164 LEU Chi-restraints excluded: chain P residue 183 ILE Chi-restraints excluded: chain P residue 185 LEU Chi-restraints excluded: chain P residue 206 GLU Chi-restraints excluded: chain P residue 243 VAL Chi-restraints excluded: chain P residue 263 VAL Chi-restraints excluded: chain P residue 276 LYS Chi-restraints excluded: chain h residue 387 MET Chi-restraints excluded: chain i residue 426 MET Chi-restraints excluded: chain j residue 359 ILE Chi-restraints excluded: chain k residue 419 LEU Chi-restraints excluded: chain l residue 418 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 48 optimal weight: 40.0000 chunk 328 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 81 optimal weight: 20.0000 chunk 33 optimal weight: 0.9990 chunk 489 optimal weight: 1.9990 chunk 373 optimal weight: 0.5980 chunk 65 optimal weight: 0.0670 chunk 477 optimal weight: 7.9990 chunk 442 optimal weight: 2.9990 chunk 406 optimal weight: 0.6980 overall best weight: 0.8722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 GLN ** A 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 207 GLN E 139 HIS E 211 GLN E 242 GLN ** F 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 HIS F 150 GLN F 266 ASN ** G 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 356 HIS I 148 GLN I 150 GLN J 17 GLN J 129 GLN ** K 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 64 GLN K 238 GLN ** L 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 242 GLN ** N 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 266 ASN ** O 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 82 ASN ** O 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.206107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.155021 restraints weight = 64754.389| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 2.80 r_work: 0.3645 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.268 44538 Z= 0.170 Angle : 0.658 23.611 60392 Z= 0.337 Chirality : 0.043 0.196 6606 Planarity : 0.004 0.063 7462 Dihedral : 13.161 73.666 6360 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.72 % Allowed : 19.69 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.12), residues: 5058 helix: 2.11 (0.10), residues: 2706 sheet: 0.35 (0.17), residues: 908 loop : -1.30 (0.15), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG L 155 TYR 0.019 0.002 TYR O 70 PHE 0.017 0.001 PHE O 26 TRP 0.027 0.002 TRP K 1 HIS 0.025 0.002 HIS O 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 (44474) covalent geometry : angle 0.63418 / 0.33 (60368) hydrogen bonds : bond 0.04140 / 2.81 ( 2434) hydrogen bonds : angle 4.05673 / 2.95 ( 7039) metal coordination : bond 0.05698 / 4.52 ( 64) metal coordination : angle 8.78551 / 7.17 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19242.05 seconds wall clock time: 326 minutes 34.09 seconds (19594.09 seconds total)