Starting phenix.real_space_refine on Sat Feb 24 13:28:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvu_12613/02_2024/7nvu_12613.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvu_12613/02_2024/7nvu_12613.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvu_12613/02_2024/7nvu_12613.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvu_12613/02_2024/7nvu_12613.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvu_12613/02_2024/7nvu_12613.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nvu_12613/02_2024/7nvu_12613.pdb" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.981 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: 7 Type Number sf(0) Gaussians Zn 10 6.06 5 P 89 5.49 5 Mg 1 5.21 5 S 250 5.16 5 C 27644 2.51 5 N 7777 2.21 5 O 8469 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 404": "OE1" <-> "OE2" Residue "A GLU 500": "OE1" <-> "OE2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 836": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 935": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 252": "OD1" <-> "OD2" Residue "Q ASP 132": "OD1" <-> "OD2" Residue "Q PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 8": "OD1" <-> "OD2" Residue "V PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 23": "NH1" <-> "NH2" Residue "W PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 29": "OE1" <-> "OE2" Residue "W ASP 35": "OD1" <-> "OD2" Residue "W GLU 46": "OE1" <-> "OE2" Residue "W GLU 50": "OE1" <-> "OE2" Residue "W ASP 69": "OD1" <-> "OD2" Residue "W ASP 83": "OD1" <-> "OD2" Residue "W PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 115": "OE1" <-> "OE2" Residue "W PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 164": "OD1" <-> "OD2" Residue "W ASP 172": "OD1" <-> "OD2" Residue "W GLU 182": "OE1" <-> "OE2" Residue "W ARG 192": "NH1" <-> "NH2" Residue "W ASP 196": "OD1" <-> "OD2" Residue "X ASP 93": "OD1" <-> "OD2" Residue "X GLU 101": "OE1" <-> "OE2" Residue "X ASP 104": "OD1" <-> "OD2" Residue "X ASP 110": "OD1" <-> "OD2" Residue "X GLU 122": "OE1" <-> "OE2" Residue "X TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 172": "OE1" <-> "OE2" Residue "X ASP 213": "OD1" <-> "OD2" Residue "X GLU 214": "OE1" <-> "OE2" Residue "X GLU 215": "OE1" <-> "OE2" Residue "X GLU 235": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 44240 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 11274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1423, 11274 Classifications: {'peptide': 1423} Link IDs: {'PCIS': 3, 'PTRANS': 67, 'TRANS': 1352} Chain breaks: 4 Chain: "B" Number of atoms: 9076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1136, 9076 Classifications: {'peptide': 1136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 53, 'TRANS': 1082} Chain breaks: 2 Chain: "C" Number of atoms: 2059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2059 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 15, 'TRANS': 241} Chain breaks: 1 Chain: "D" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1050 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 3, 'TRANS': 124} Chain: "E" Number of atoms: 1721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1721 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 636 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "G" Number of atoms: 1351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1351 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain: "H" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1186 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "I" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 928 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain: "J" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 507 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 373 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "M" Number of atoms: 2301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2301 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 15, 'TRANS': 282} Chain breaks: 1 Chain: "N" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 914 Classifications: {'DNA': 44} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 43} Chain breaks: 1 Chain: "O" Number of atoms: 1422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1422 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 9, 'TRANS': 169} Chain: "Q" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1138 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 7, 'TRANS': 130} Chain breaks: 1 Chain: "R" Number of atoms: 1788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1788 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 7, 'TRANS': 214} Chain breaks: 1 Chain: "T" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 911 Classifications: {'DNA': 46} Link IDs: {'rna3p': 45} Unresolved chain links: 1 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DG:plan': 1, ' DG:plan2': 1} Unresolved non-hydrogen planarities: 14 Chain: "U" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 930 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 2, 'TRANS': 110} Chain breaks: 1 Chain: "V" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 806 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 1, 'TRANS': 97} Chain: "W" Number of atoms: 1535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1535 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 5, 'TRANS': 181} Chain: "X" Number of atoms: 1403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1403 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 5, 'TRANS': 165} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" 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: "W" 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 464 SG CYS A 71 100.911 106.992 67.692 1.00 31.19 S ATOM 486 SG CYS A 74 99.467 105.949 64.422 1.00 39.86 S ATOM 533 SG CYS A 81 98.849 103.875 67.448 1.00 31.84 S ATOM 768 SG CYS A 111 138.084 78.462 71.813 1.00 64.47 S ATOM 796 SG CYS A 114 140.458 79.737 68.929 1.00 67.75 S ATOM 1109 SG CYS A 154 140.282 76.135 70.096 1.00 79.92 S ATOM 1132 SG CYS A 184 141.931 79.216 71.878 1.00 79.38 S ATOM 19919 SG CYS B1119 110.251 97.095 54.840 1.00 19.77 S ATOM 19941 SG CYS B1122 111.263 95.500 58.096 1.00 31.20 S ATOM 20056 SG CYS B1137 110.702 99.189 57.888 1.00 43.68 S ATOM 20077 SG CYS B1140 113.667 97.579 56.240 1.00 49.84 S ATOM 21044 SG CYS C 88 32.361 101.033 72.561 1.00 30.76 S ATOM 21057 SG CYS C 90 34.820 103.254 74.541 1.00 50.98 S ATOM 21092 SG CYS C 94 31.599 102.667 75.813 1.00 25.33 S ATOM 21114 SG CYS C 97 33.997 99.818 75.736 1.00 23.56 S ATOM 28400 SG CYS I 17 126.950 42.135 122.346 1.00 76.73 S ATOM 28424 SG CYS I 20 127.498 45.607 121.885 1.00 83.36 S ATOM 28585 SG CYS I 39 128.475 43.197 119.089 1.00 81.10 S ATOM 28610 SG CYS I 42 130.632 43.490 122.847 1.00 88.26 S ATOM 28962 SG CYS I 86 87.063 23.293 121.178 1.00 60.43 S ATOM 28986 SG CYS I 89 85.070 23.587 124.372 1.00 76.35 S ATOM 29190 SG CYS I 114 85.182 26.465 122.059 1.00 48.41 S ATOM 29225 SG CYS I 119 88.194 25.465 124.030 1.00 63.36 S ATOM 29336 SG CYS J 7 41.192 72.302 89.249 1.00 20.68 S ATOM 29360 SG CYS J 10 37.931 72.015 87.279 1.00 20.68 S ATOM 29624 SG CYS J 44 40.022 68.921 88.245 1.00 2.84 S ATOM 29630 SG CYS J 45 37.936 70.875 90.592 1.00 20.68 S ATOM 30750 SG CYS L 19 61.822 104.384 110.330 1.00 31.60 S ATOM 30769 SG CYS L 22 59.069 105.930 112.350 1.00 38.25 S ATOM 30886 SG CYS L 36 61.809 107.960 111.287 1.00 31.17 S ATOM 30912 SG CYS L 39 62.486 105.398 113.802 1.00 47.93 S ATOM 31094 SG CYS M 15 76.406 113.441 60.741 1.00 62.91 S ATOM 31241 SG CYS M 34 74.000 113.311 63.603 1.00 46.82 S ATOM 31263 SG CYS M 37 73.119 111.798 60.162 1.00 54.45 S ATOM 42289 SG CYS W 129 109.279 131.113 59.019 1.00113.62 S ATOM 42481 SG CYS W 154 105.723 128.779 58.778 1.00114.80 S ATOM 42505 SG CYS W 157 105.767 131.602 60.984 1.00112.77 S Time building chain proxies: 21.93, per 1000 atoms: 0.50 Number of scatterers: 44240 At special positions: 0 Unit cell: (175.35, 171.15, 182.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 10 29.99 S 250 16.00 P 89 15.00 Mg 1 11.99 O 8469 8.00 N 7777 7.00 C 27644 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 - 3.50 Amino acid : False - 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: 17.53 Conformation dependent library (CDL) restraints added in 7.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" NE2 HIS A 84 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 74 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 71 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 81 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 114 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 184 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 154 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 111 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1122 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1119 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1137 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1140 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 94 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 97 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 17 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 39 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 42 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 114 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 36 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 22 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 39 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 19 " pdb=" ZN M 401 " pdb="ZN ZN M 401 " - pdb=" NE2 HIS M 18 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 37 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 34 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 15 " pdb=" ZN W 501 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 157 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 154 " pdb="ZN ZN W 501 " - pdb=" SG CYS W 129 " Number of angles added : 48 10466 Ramachandran restraints generated. 5233 Oldfield, 0 Emsley, 5233 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9990 Finding SS restraints... Secondary structure from input PDB file: 191 helices and 0 sheets defined 36.0% alpha, 0.0% beta 38 base pairs and 72 stacking pairs defined. Time for finding SS restraints: 15.02 Creating SS restraints... Processing helix chain 'A' and resid 28 through 34 Processing helix chain 'A' and resid 97 through 109 removed outlier: 4.673A pdb=" N VAL A 101 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N LYS A 102 " --> pdb=" O GLY A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 133 Processing helix chain 'A' and resid 137 through 150 removed outlier: 3.534A pdb=" N THR A 142 " --> pdb=" O LYS A 138 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLY A 150 " --> pdb=" O ASP A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 227 Processing helix chain 'A' and resid 230 through 235 Processing helix chain 'A' and resid 245 through 248 Processing helix chain 'A' and resid 259 through 261 No H-bonds generated for 'chain 'A' and resid 259 through 261' Processing helix chain 'A' and resid 275 through 296 Processing helix chain 'A' and resid 300 through 318 removed outlier: 3.631A pdb=" N VAL A 318 " --> pdb=" O VAL A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 382 through 387 Processing helix chain 'A' and resid 399 through 408 Processing helix chain 'A' and resid 435 through 438 No H-bonds generated for 'chain 'A' and resid 435 through 438' Processing helix chain 'A' and resid 466 through 468 No H-bonds generated for 'chain 'A' and resid 466 through 468' Processing helix chain 'A' and resid 487 through 492 removed outlier: 3.588A pdb=" N THR A 490 " --> pdb=" O SER A 487 " (cutoff:3.500A) Proline residue: A 491 - end of helix No H-bonds generated for 'chain 'A' and resid 487 through 492' Processing helix chain 'A' and resid 509 through 518 Processing helix chain 'A' and resid 521 through 524 Processing helix chain 'A' and resid 539 through 548 Processing helix chain 'A' and resid 557 through 566 removed outlier: 3.909A pdb=" N PHE A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 595 Processing helix chain 'A' and resid 611 through 613 No H-bonds generated for 'chain 'A' and resid 611 through 613' Processing helix chain 'A' and resid 642 through 645 No H-bonds generated for 'chain 'A' and resid 642 through 645' Processing helix chain 'A' and resid 652 through 660 Processing helix chain 'A' and resid 662 through 683 removed outlier: 4.112A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 692 Processing helix chain 'A' and resid 696 through 721 Processing helix chain 'A' and resid 733 through 759 Processing helix chain 'A' and resid 765 through 771 Processing helix chain 'A' and resid 778 through 785 Processing helix chain 'A' and resid 833 through 868 removed outlier: 3.534A pdb=" N GLU A 845 " --> pdb=" O MET A 841 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY A 846 " --> pdb=" O GLY A 842 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE A 860 " --> pdb=" O GLU A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 893 No H-bonds generated for 'chain 'A' and resid 891 through 893' Processing helix chain 'A' and resid 913 through 920 Processing helix chain 'A' and resid 927 through 933 Processing helix chain 'A' and resid 936 through 944 removed outlier: 3.934A pdb=" N ASP A 941 " --> pdb=" O ASP A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 969 Processing helix chain 'A' and resid 983 through 993 Processing helix chain 'A' and resid 1006 through 1019 Processing helix chain 'A' and resid 1028 through 1037 Processing helix chain 'A' and resid 1039 through 1048 Processing helix chain 'A' and resid 1051 through 1056 Processing helix chain 'A' and resid 1062 through 1079 Processing helix chain 'A' and resid 1087 through 1101 Proline residue: A1098 - end of helix removed outlier: 4.144A pdb=" N GLN A1101 " --> pdb=" O GLU A1097 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1128 Processing helix chain 'A' and resid 1151 through 1161 removed outlier: 3.578A pdb=" N ILE A1157 " --> pdb=" O ARG A1153 " (cutoff:3.500A) Processing helix chain 'A' and resid 1187 through 1198 removed outlier: 4.353A pdb=" N TRP A1192 " --> pdb=" O GLU A1188 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASN A1194 " --> pdb=" O GLN A1190 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N VAL A1195 " --> pdb=" O GLU A1191 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR A1196 " --> pdb=" O TRP A1192 " (cutoff:3.500A) Processing helix chain 'A' and resid 1218 through 1224 Processing helix chain 'A' and resid 1228 through 1239 Processing helix chain 'A' and resid 1263 through 1266 No H-bonds generated for 'chain 'A' and resid 1263 through 1266' Processing helix chain 'A' and resid 1283 through 1294 Processing helix chain 'A' and resid 1343 through 1348 removed outlier: 3.521A pdb=" N SER A1348 " --> pdb=" O MET A1344 " (cutoff:3.500A) Processing helix chain 'A' and resid 1362 through 1369 Processing helix chain 'A' and resid 1371 through 1389 removed outlier: 4.804A pdb=" N ASP A1389 " --> pdb=" O VAL A1385 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1406 Processing helix chain 'A' and resid 1416 through 1419 No H-bonds generated for 'chain 'A' and resid 1416 through 1419' Processing helix chain 'A' and resid 1426 through 1432 Processing helix chain 'A' and resid 1435 through 1444 Processing helix chain 'A' and resid 1454 through 1459 Processing helix chain 'A' and resid 1467 through 1469 No H-bonds generated for 'chain 'A' and resid 1467 through 1469' Processing helix chain 'A' and resid 1477 through 1481 Processing helix chain 'B' and resid 19 through 37 removed outlier: 4.461A pdb=" N GLN B 23 " --> pdb=" O PRO B 19 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N GLU B 24 " --> pdb=" O ASP B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 52 Processing helix chain 'B' and resid 54 through 61 Processing helix chain 'B' and resid 110 through 116 Processing helix chain 'B' and resid 168 through 174 Processing helix chain 'B' and resid 247 through 252 Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 281 through 288 Processing helix chain 'B' and resid 295 through 307 removed outlier: 3.530A pdb=" N MET B 300 " --> pdb=" O GLU B 296 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL B 301 " --> pdb=" O MET B 297 " (cutoff:3.500A) Proline residue: B 303 - end of helix Processing helix chain 'B' and resid 314 through 324 removed outlier: 3.805A pdb=" N ARG B 324 " --> pdb=" O PHE B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 345 Processing helix chain 'B' and resid 358 through 377 Processing helix chain 'B' and resid 396 through 424 removed outlier: 3.629A pdb=" N GLY B 406 " --> pdb=" O PHE B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 434 No H-bonds generated for 'chain 'B' and resid 431 through 434' Processing helix chain 'B' and resid 438 through 450 Processing helix chain 'B' and resid 475 through 483 Processing helix chain 'B' and resid 496 through 499 No H-bonds generated for 'chain 'B' and resid 496 through 499' Processing helix chain 'B' and resid 503 through 505 No H-bonds generated for 'chain 'B' and resid 503 through 505' Processing helix chain 'B' and resid 539 through 547 Processing helix chain 'B' and resid 558 through 561 Processing helix chain 'B' and resid 580 through 593 Processing helix chain 'B' and resid 637 through 644 Processing helix chain 'B' and resid 653 through 659 Processing helix chain 'B' and resid 667 through 672 removed outlier: 3.618A pdb=" N GLU B 671 " --> pdb=" O THR B 667 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N THR B 672 " --> pdb=" O LEU B 668 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 667 through 672' Processing helix chain 'B' and resid 679 through 682 No H-bonds generated for 'chain 'B' and resid 679 through 682' Processing helix chain 'B' and resid 700 through 703 Processing helix chain 'B' and resid 708 through 710 No H-bonds generated for 'chain 'B' and resid 708 through 710' Processing helix chain 'B' and resid 714 through 716 No H-bonds generated for 'chain 'B' and resid 714 through 716' Processing helix chain 'B' and resid 719 through 731 removed outlier: 3.739A pdb=" N LYS B 730 " --> pdb=" O SER B 726 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN B 731 " --> pdb=" O ALA B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 765 Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 969 through 975 Proline residue: B 973 - end of helix Processing helix chain 'B' and resid 978 through 993 Processing helix chain 'B' and resid 1008 through 1018 removed outlier: 3.581A pdb=" N ASP B1017 " --> pdb=" O ASN B1013 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N TYR B1018 " --> pdb=" O LEU B1014 " (cutoff:3.500A) Processing helix chain 'B' and resid 1055 through 1057 No H-bonds generated for 'chain 'B' and resid 1055 through 1057' Processing helix chain 'B' and resid 1088 through 1097 Processing helix chain 'B' and resid 1100 through 1107 Processing helix chain 'B' and resid 1153 through 1165 Processing helix chain 'C' and resid 28 through 40 Processing helix chain 'C' and resid 61 through 70 Processing helix chain 'C' and resid 78 through 81 No H-bonds generated for 'chain 'C' and resid 78 through 81' Processing helix chain 'C' and resid 117 through 119 No H-bonds generated for 'chain 'C' and resid 117 through 119' Processing helix chain 'C' and resid 174 through 176 No H-bonds generated for 'chain 'C' and resid 174 through 176' Processing helix chain 'C' and resid 200 through 202 No H-bonds generated for 'chain 'C' and resid 200 through 202' Processing helix chain 'C' and resid 241 through 270 Processing helix chain 'D' and resid 34 through 49 Processing helix chain 'D' and resid 59 through 71 Processing helix chain 'D' and resid 77 through 89 Processing helix chain 'D' and resid 94 through 103 Processing helix chain 'D' and resid 108 through 114 Processing helix chain 'D' and resid 116 through 118 No H-bonds generated for 'chain 'D' and resid 116 through 118' Processing helix chain 'D' and resid 124 through 137 Processing helix chain 'E' and resid 3 through 23 Processing helix chain 'E' and resid 30 through 33 No H-bonds generated for 'chain 'E' and resid 30 through 33' Processing helix chain 'E' and resid 37 through 44 Processing helix chain 'E' and resid 84 through 97 Processing helix chain 'E' and resid 112 through 120 removed outlier: 3.711A pdb=" N VAL E 119 " --> pdb=" O LYS E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 136 Processing helix chain 'E' and resid 139 through 141 No H-bonds generated for 'chain 'E' and resid 139 through 141' Processing helix chain 'E' and resid 153 through 163 Processing helix chain 'E' and resid 167 through 169 No H-bonds generated for 'chain 'E' and resid 167 through 169' Processing helix chain 'E' and resid 178 through 183 Processing helix chain 'F' and resid 59 through 74 Processing helix chain 'F' and resid 89 through 99 Processing helix chain 'G' and resid 15 through 17 No H-bonds generated for 'chain 'G' and resid 15 through 17' Processing helix chain 'G' and resid 22 through 34 Processing helix chain 'H' and resid 84 through 87 Processing helix chain 'H' and resid 129 through 132 Processing helix chain 'I' and resid 64 through 67 No H-bonds generated for 'chain 'I' and resid 64 through 67' Processing helix chain 'I' and resid 70 through 74 Processing helix chain 'J' and resid 18 through 26 Processing helix chain 'J' and resid 31 through 37 Processing helix chain 'J' and resid 43 through 50 Processing helix chain 'J' and resid 56 through 61 removed outlier: 3.635A pdb=" N ASN J 61 " --> pdb=" O GLU J 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 9 removed outlier: 3.538A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 6 through 9' Processing helix chain 'K' and resid 40 through 52 removed outlier: 3.734A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 114 Processing helix chain 'M' and resid 90 through 92 No H-bonds generated for 'chain 'M' and resid 90 through 92' Processing helix chain 'M' and resid 109 through 127 Processing helix chain 'M' and resid 132 through 148 Processing helix chain 'M' and resid 156 through 170 Processing helix chain 'M' and resid 177 through 182 Processing helix chain 'M' and resid 188 through 202 Processing helix chain 'M' and resid 211 through 213 No H-bonds generated for 'chain 'M' and resid 211 through 213' Processing helix chain 'M' and resid 215 through 222 Processing helix chain 'M' and resid 226 through 242 Processing helix chain 'M' and resid 250 through 263 Processing helix chain 'M' and resid 271 through 278 Processing helix chain 'M' and resid 282 through 293 Processing helix chain 'M' and resid 296 through 299 No H-bonds generated for 'chain 'M' and resid 296 through 299' Processing helix chain 'M' and resid 310 through 312 No H-bonds generated for 'chain 'M' and resid 310 through 312' Processing helix chain 'O' and resid 180 through 186 Processing helix chain 'O' and resid 227 through 244 Processing helix chain 'O' and resid 270 through 276 Processing helix chain 'O' and resid 318 through 335 Proline residue: O 330 - end of helix removed outlier: 3.627A pdb=" N PHE O 335 " --> pdb=" O ILE O 331 " (cutoff:3.500A) Processing helix chain 'Q' and resid 6 through 9 Processing helix chain 'Q' and resid 33 through 35 No H-bonds generated for 'chain 'Q' and resid 33 through 35' Processing helix chain 'Q' and resid 157 through 165 removed outlier: 3.820A pdb=" N GLU Q 162 " --> pdb=" O GLU Q 158 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU Q 165 " --> pdb=" O GLU Q 161 " (cutoff:3.500A) Processing helix chain 'Q' and resid 173 through 179 removed outlier: 4.481A pdb=" N MET Q 177 " --> pdb=" O HIS Q 173 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLN Q 178 " --> pdb=" O PHE Q 174 " (cutoff:3.500A) Processing helix chain 'R' and resid 10 through 13 No H-bonds generated for 'chain 'R' and resid 10 through 13' Processing helix chain 'R' and resid 25 through 34 Processing helix chain 'R' and resid 60 through 63 No H-bonds generated for 'chain 'R' and resid 60 through 63' Processing helix chain 'R' and resid 123 through 137 removed outlier: 3.788A pdb=" N LEU R 127 " --> pdb=" O ASN R 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 160 through 172 Processing helix chain 'R' and resid 180 through 193 removed outlier: 3.848A pdb=" N LYS R 193 " --> pdb=" O SER R 189 " (cutoff:3.500A) Processing helix chain 'R' and resid 199 through 206 removed outlier: 3.786A pdb=" N ASP R 204 " --> pdb=" O LYS R 200 " (cutoff:3.500A) Processing helix chain 'R' and resid 210 through 220 removed outlier: 3.687A pdb=" N ILE R 220 " --> pdb=" O ILE R 216 " (cutoff:3.500A) Processing helix chain 'U' and resid 10 through 31 removed outlier: 4.459A pdb=" N ASP U 27 " --> pdb=" O ASN U 23 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ILE U 28 " --> pdb=" O ASP U 24 " (cutoff:3.500A) Processing helix chain 'U' and resid 36 through 50 removed outlier: 3.553A pdb=" N LYS U 49 " --> pdb=" O TRP U 46 " (cutoff:3.500A) Processing helix chain 'U' and resid 325 through 329 Processing helix chain 'V' and resid 6 through 8 No H-bonds generated for 'chain 'V' and resid 6 through 8' Processing helix chain 'V' and resid 10 through 24 Processing helix chain 'V' and resid 30 through 51 Processing helix chain 'W' and resid 12 through 25 Processing helix chain 'W' and resid 28 through 39 Processing helix chain 'W' and resid 45 through 52 Processing helix chain 'W' and resid 56 through 69 Processing helix chain 'W' and resid 96 through 123 removed outlier: 3.626A pdb=" N ASN W 101 " --> pdb=" O ARG W 97 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG W 119 " --> pdb=" O GLU W 115 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N THR W 122 " --> pdb=" O GLU W 118 " (cutoff:3.500A) Processing helix chain 'W' and resid 138 through 144 Processing helix chain 'W' and resid 164 through 183 removed outlier: 3.856A pdb=" N MET W 168 " --> pdb=" O ASP W 164 " (cutoff:3.500A) Proline residue: W 169 - end of helix removed outlier: 3.751A pdb=" N ASP W 172 " --> pdb=" O MET W 168 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA W 173 " --> pdb=" O PRO W 169 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG W 174 " --> pdb=" O LYS W 170 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR W 175 " --> pdb=" O LYS W 171 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA W 178 " --> pdb=" O ARG W 174 " (cutoff:3.500A) Processing helix chain 'W' and resid 185 through 194 Processing helix chain 'X' and resid 77 through 90 Processing helix chain 'X' and resid 99 through 105 removed outlier: 3.670A pdb=" N GLU X 105 " --> pdb=" O GLU X 101 " (cutoff:3.500A) Processing helix chain 'X' and resid 113 through 121 Processing helix chain 'X' and resid 123 through 126 No H-bonds generated for 'chain 'X' and resid 123 through 126' Processing helix chain 'X' and resid 148 through 161 Processing helix chain 'X' and resid 168 through 174 Processing helix chain 'X' and resid 178 through 188 removed outlier: 5.967A pdb=" N ASP X 187 " --> pdb=" O LYS X 183 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N GLN X 188 " --> pdb=" O ALA X 184 " (cutoff:3.500A) Processing helix chain 'X' and resid 214 through 222 Processing helix chain 'X' and resid 230 through 240 removed outlier: 3.870A pdb=" N LEU X 237 " --> pdb=" O ILE X 233 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS X 238 " --> pdb=" O GLU X 234 " (cutoff:3.500A) 1098 hydrogen bonds defined for protein. 3225 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 103 hydrogen bonds 206 hydrogen bond angles 0 basepair planarities 38 basepair parallelities 72 stacking parallelities Total time for adding SS restraints: 15.97 Time building geometry restraints manager: 18.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 14384 1.34 - 1.46: 7419 1.46 - 1.58: 22859 1.58 - 1.70: 175 1.70 - 1.82: 394 Bond restraints: 45231 Sorted by residual: bond pdb=" N MET V 1 " pdb=" CA MET V 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.98e+00 bond pdb=" N MET G 1 " pdb=" CA MET G 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 bond pdb=" N MET K 1 " pdb=" CA MET K 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.93e+00 bond pdb=" N MET J 1 " pdb=" CA MET J 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.64e+00 bond pdb=" CB TRP B 453 " pdb=" CG TRP B 453 " ideal model delta sigma weight residual 1.498 1.456 0.042 3.10e-02 1.04e+03 1.83e+00 ... (remaining 45226 not shown) Histogram of bond angle deviations from ideal: 99.97 - 106.78: 1761 106.78 - 113.59: 24928 113.59 - 120.40: 17094 120.40 - 127.20: 17075 127.20 - 134.01: 576 Bond angle restraints: 61434 Sorted by residual: angle pdb=" CG ARG A 483 " pdb=" CD ARG A 483 " pdb=" NE ARG A 483 " ideal model delta sigma weight residual 112.00 119.15 -7.15 2.20e+00 2.07e-01 1.06e+01 angle pdb=" N GLY B 150 " pdb=" CA GLY B 150 " pdb=" C GLY B 150 " ideal model delta sigma weight residual 110.46 114.09 -3.63 1.43e+00 4.89e-01 6.44e+00 angle pdb=" N ILE A 682 " pdb=" CA ILE A 682 " pdb=" C ILE A 682 " ideal model delta sigma weight residual 111.45 109.11 2.34 9.30e-01 1.16e+00 6.36e+00 angle pdb=" N ARG O 205 " pdb=" CA ARG O 205 " pdb=" C ARG O 205 " ideal model delta sigma weight residual 111.36 113.97 -2.61 1.09e+00 8.42e-01 5.74e+00 angle pdb=" C3' DA T -34 " pdb=" C2' DA T -34 " pdb=" C1' DA T -34 " ideal model delta sigma weight residual 101.60 105.19 -3.59 1.50e+00 4.44e-01 5.74e+00 ... (remaining 61429 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 24472 17.97 - 35.94: 2279 35.94 - 53.90: 524 53.90 - 71.87: 159 71.87 - 89.84: 55 Dihedral angle restraints: 27489 sinusoidal: 12064 harmonic: 15425 Sorted by residual: dihedral pdb=" CA VAL A 538 " pdb=" C VAL A 538 " pdb=" N GLN A 539 " pdb=" CA GLN A 539 " ideal model delta harmonic sigma weight residual -180.00 -145.82 -34.18 0 5.00e+00 4.00e-02 4.67e+01 dihedral pdb=" CA LYS O 297 " pdb=" C LYS O 297 " pdb=" N PRO O 298 " pdb=" CA PRO O 298 " ideal model delta harmonic sigma weight residual 180.00 154.25 25.75 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA ASN A1129 " pdb=" C ASN A1129 " pdb=" N ILE A1130 " pdb=" CA ILE A1130 " ideal model delta harmonic sigma weight residual -180.00 -155.10 -24.90 0 5.00e+00 4.00e-02 2.48e+01 ... (remaining 27486 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 4335 0.028 - 0.057: 1573 0.057 - 0.085: 443 0.085 - 0.113: 393 0.113 - 0.141: 105 Chirality restraints: 6849 Sorted by residual: chirality pdb=" CA ILE A 419 " pdb=" N ILE A 419 " pdb=" C ILE A 419 " pdb=" CB ILE A 419 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 5.00e-01 chirality pdb=" CA ILE J 3 " pdb=" N ILE J 3 " pdb=" C ILE J 3 " pdb=" CB ILE J 3 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.99e-01 chirality pdb=" CA PRO B1001 " pdb=" N PRO B1001 " pdb=" C PRO B1001 " pdb=" CB PRO B1001 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.96e-01 ... (remaining 6846 not shown) Planarity restraints: 7660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B1048 " 0.018 2.00e-02 2.50e+03 1.77e-02 6.24e+00 pdb=" CG TYR B1048 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TYR B1048 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR B1048 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR B1048 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR B1048 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B1048 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR B1048 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS O 297 " 0.036 5.00e-02 4.00e+02 5.44e-02 4.73e+00 pdb=" N PRO O 298 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO O 298 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO O 298 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B1168 " -0.032 5.00e-02 4.00e+02 4.88e-02 3.81e+00 pdb=" N PRO B1169 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO B1169 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B1169 " -0.027 5.00e-02 4.00e+02 ... (remaining 7657 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 216 2.49 - 3.09: 32437 3.09 - 3.70: 70752 3.70 - 4.30: 108665 4.30 - 4.90: 172328 Nonbonded interactions: 384398 Sorted by model distance: nonbonded pdb=" OD2 ASP H 8 " pdb=" OG SER H 32 " model vdw 1.889 2.440 nonbonded pdb=" NH2 ARG C 67 " pdb=" O ILE J 3 " model vdw 1.900 2.520 nonbonded pdb=" OD2 ASP E 3 " pdb=" OG SER E 49 " model vdw 2.008 2.440 nonbonded pdb=" O MET A 535 " pdb=" OH TYR A 669 " model vdw 2.022 2.440 nonbonded pdb=" OG1 THR B 474 " pdb=" O ALA B 732 " model vdw 2.038 2.440 ... (remaining 384393 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 4.580 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: 0.040 Extract box with map and model: 21.540 Check model and map are aligned: 0.690 Set scattering table: 0.380 Process input model: 127.520 Find NCS groups from input model: 1.330 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 168.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 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 : 0.003 0.043 45231 Z= 0.197 Angle : 0.454 7.147 61434 Z= 0.262 Chirality : 0.040 0.141 6849 Planarity : 0.003 0.054 7660 Dihedral : 15.453 89.841 17499 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.12), residues: 5233 helix: 1.96 (0.12), residues: 1939 sheet: 0.62 (0.18), residues: 851 loop : 0.33 (0.13), residues: 2443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 203 HIS 0.007 0.001 HIS M 18 PHE 0.032 0.001 PHE A 458 TYR 0.043 0.001 TYR B1048 ARG 0.005 0.000 ARG A 483 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10466 Ramachandran restraints generated. 5233 Oldfield, 0 Emsley, 5233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10466 Ramachandran restraints generated. 5233 Oldfield, 0 Emsley, 5233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 918 residues out of total 4684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 918 time to evaluate : 5.170 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.7804 (mmt90) cc_final: 0.7559 (mpt-90) REVERT: A 220 ARG cc_start: 0.8257 (tpt-90) cc_final: 0.7750 (tpt170) REVERT: A 439 HIS cc_start: 0.7424 (t70) cc_final: 0.7135 (m-70) REVERT: A 845 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7491 (mm-30) REVERT: A 1306 LYS cc_start: 0.7982 (ttmm) cc_final: 0.7737 (tppt) REVERT: A 1472 ASP cc_start: 0.7669 (m-30) cc_final: 0.7420 (m-30) REVERT: B 677 MET cc_start: 0.9008 (tpp) cc_final: 0.8562 (tpp) REVERT: B 1104 ARG cc_start: 0.8580 (ttt-90) cc_final: 0.8315 (ttp-170) REVERT: E 23 ASP cc_start: 0.8169 (m-30) cc_final: 0.7953 (m-30) REVERT: E 116 GLN cc_start: 0.8295 (tp40) cc_final: 0.7833 (tp40) REVERT: E 137 ILE cc_start: 0.8499 (pt) cc_final: 0.8277 (pt) REVERT: F 59 LYS cc_start: 0.9136 (ptpt) cc_final: 0.8905 (ptmt) REVERT: G 117 MET cc_start: -0.0139 (mmm) cc_final: -0.0980 (tmm) REVERT: H 111 ARG cc_start: 0.7990 (mmm-85) cc_final: 0.7672 (mtp-110) REVERT: H 123 MET cc_start: 0.8965 (ttp) cc_final: 0.8718 (ttp) REVERT: I 34 ILE cc_start: 0.8278 (tp) cc_final: 0.8032 (pp) REVERT: I 37 TYR cc_start: 0.8607 (m-80) cc_final: 0.8401 (m-80) REVERT: I 56 ASN cc_start: 0.8679 (t0) cc_final: 0.8349 (t0) REVERT: L 58 ARG cc_start: 0.7867 (mtt180) cc_final: 0.7600 (mtt180) REVERT: M 52 TRP cc_start: 0.8354 (p90) cc_final: 0.8009 (p90) REVERT: M 86 LYS cc_start: 0.7711 (mttt) cc_final: 0.7433 (ttpp) REVERT: M 190 GLU cc_start: 0.7639 (tp30) cc_final: 0.7364 (tp30) REVERT: M 300 PHE cc_start: 0.8196 (m-80) cc_final: 0.7876 (m-80) REVERT: O 277 HIS cc_start: 0.8618 (m-70) cc_final: 0.8369 (m90) REVERT: Q 111 LYS cc_start: 0.8259 (ttpt) cc_final: 0.7926 (tptt) outliers start: 0 outliers final: 1 residues processed: 918 average time/residue: 1.8529 time to fit residues: 2033.3174 Evaluate side-chains 633 residues out of total 4684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 632 time to evaluate : 4.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 130 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 526 random chunks: chunk 444 optimal weight: 0.9990 chunk 398 optimal weight: 1.9990 chunk 221 optimal weight: 0.9990 chunk 136 optimal weight: 2.9990 chunk 268 optimal weight: 1.9990 chunk 212 optimal weight: 1.9990 chunk 412 optimal weight: 5.9990 chunk 159 optimal weight: 4.9990 chunk 250 optimal weight: 3.9990 chunk 306 optimal weight: 2.9990 chunk 477 optimal weight: 0.5980 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 ASN A 711 GLN A 722 ASN A 861 GLN A1077 ASN A1299 GLN ** A1310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 HIS B 500 GLN B 552 ASN B 585 ASN ** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1068 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN C 111 GLN C 217 GLN H 76 ASN J 52 HIS K 89 ASN ** M 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 116 ASN M 140 ASN O 277 HIS ** O 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 168 ASN R 144 GLN ** W 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 45231 Z= 0.347 Angle : 0.584 13.758 61434 Z= 0.305 Chirality : 0.045 0.245 6849 Planarity : 0.004 0.055 7660 Dihedral : 12.006 59.889 6736 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.11 % Allowed : 9.99 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.12), residues: 5233 helix: 1.48 (0.12), residues: 1963 sheet: 0.69 (0.18), residues: 834 loop : 0.18 (0.13), residues: 2436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 203 HIS 0.007 0.001 HIS C 60 PHE 0.033 0.002 PHE A 458 TYR 0.023 0.002 TYR A1482 ARG 0.010 0.001 ARG A 483 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10466 Ramachandran restraints generated. 5233 Oldfield, 0 Emsley, 5233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10466 Ramachandran restraints generated. 5233 Oldfield, 0 Emsley, 5233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 756 residues out of total 4684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 657 time to evaluate : 5.778 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: symmetry clash revert: symmetry clash REVERT: A 16 ARG cc_start: 0.7843 (mmt90) cc_final: 0.7595 (mpt-90) REVERT: A 58 MET cc_start: 0.7810 (mmp) cc_final: 0.7578 (mmt) REVERT: A 67 ARG cc_start: 0.7701 (mmm160) cc_final: 0.7057 (mmm160) REVERT: A 220 ARG cc_start: 0.8221 (tpt-90) cc_final: 0.7853 (tpt170) REVERT: A 423 ASN cc_start: 0.7581 (p0) cc_final: 0.7114 (p0) REVERT: A 425 ASP cc_start: 0.7632 (m-30) cc_final: 0.7347 (m-30) REVERT: A 439 HIS cc_start: 0.7413 (t70) cc_final: 0.7101 (m-70) REVERT: A 565 MET cc_start: 0.9371 (mmm) cc_final: 0.9116 (mmm) REVERT: A 1052 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.7949 (tpt90) REVERT: A 1155 LYS cc_start: 0.7975 (ttpt) cc_final: 0.7492 (tttm) REVERT: A 1162 GLU cc_start: 0.7903 (tt0) cc_final: 0.7691 (tt0) REVERT: A 1306 LYS cc_start: 0.8020 (ttmm) cc_final: 0.7777 (tppt) REVERT: A 1440 MET cc_start: 0.8478 (mmt) cc_final: 0.7776 (mmt) REVERT: A 1472 ASP cc_start: 0.7731 (m-30) cc_final: 0.7499 (m-30) REVERT: B 287 HIS cc_start: 0.8465 (m90) cc_final: 0.8208 (m170) REVERT: B 731 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.7845 (mt0) REVERT: B 1104 ARG cc_start: 0.8626 (ttt-90) cc_final: 0.8336 (ttp-170) REVERT: C 17 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7144 (mt-10) REVERT: C 86 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7752 (ptt90) REVERT: E 116 GLN cc_start: 0.8297 (tp40) cc_final: 0.8080 (tp-100) REVERT: E 210 GLN cc_start: 0.6526 (OUTLIER) cc_final: 0.6222 (tt0) REVERT: F 59 LYS cc_start: 0.9135 (ptpt) cc_final: 0.8838 (ptmt) REVERT: F 86 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.7043 (mm-30) REVERT: G 117 MET cc_start: -0.0151 (mmm) cc_final: -0.0878 (tmm) REVERT: H 111 ARG cc_start: 0.8036 (mmm-85) cc_final: 0.7666 (mtp-110) REVERT: H 123 MET cc_start: 0.9024 (ttp) cc_final: 0.8807 (ttp) REVERT: H 147 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8181 (ttmm) REVERT: I 56 ASN cc_start: 0.8780 (t0) cc_final: 0.8391 (t0) REVERT: J 1 MET cc_start: 0.7818 (OUTLIER) cc_final: 0.7021 (mtp) REVERT: M 52 TRP cc_start: 0.8350 (p90) cc_final: 0.8025 (p90) REVERT: M 86 LYS cc_start: 0.7842 (mttt) cc_final: 0.7390 (mtpp) REVERT: M 190 GLU cc_start: 0.7456 (tp30) cc_final: 0.7196 (tp30) REVERT: M 227 GLN cc_start: 0.7310 (pm20) cc_final: 0.7017 (pm20) REVERT: M 300 PHE cc_start: 0.8081 (m-80) cc_final: 0.7738 (m-80) REVERT: M 303 ASP cc_start: 0.7530 (OUTLIER) cc_final: 0.7201 (p0) outliers start: 99 outliers final: 46 residues processed: 703 average time/residue: 1.8062 time to fit residues: 1527.9839 Evaluate side-chains 670 residues out of total 4684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 615 time to evaluate : 4.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 1052 ARG Chi-restraints excluded: chain A residue 1147 SER Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 503 ASN Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 731 GLN Chi-restraints excluded: chain B residue 828 VAL Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 892 CYS Chi-restraints excluded: chain B residue 919 CYS Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 41 LYS Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain F residue 86 GLU Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 128 ASP Chi-restraints excluded: chain H residue 130 ASN Chi-restraints excluded: chain H residue 147 LYS Chi-restraints excluded: chain I residue 82 GLU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain M residue 96 PHE Chi-restraints excluded: chain M residue 282 ASP Chi-restraints excluded: chain M residue 293 TYR Chi-restraints excluded: chain M residue 303 ASP Chi-restraints excluded: chain R residue 144 GLN Chi-restraints excluded: chain W residue 48 MET Chi-restraints excluded: chain W residue 66 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 526 random chunks: chunk 265 optimal weight: 0.9980 chunk 148 optimal weight: 1.9990 chunk 397 optimal weight: 0.9990 chunk 325 optimal weight: 0.7980 chunk 131 optimal weight: 0.9990 chunk 478 optimal weight: 30.0000 chunk 516 optimal weight: 50.0000 chunk 426 optimal weight: 5.9990 chunk 474 optimal weight: 50.0000 chunk 163 optimal weight: 3.9990 chunk 383 optimal weight: 3.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 296 ASN A 441 GLN A 861 GLN ** A1194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1299 GLN ** A1310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 GLN B 552 ASN B 585 ASN ** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 968 ASN B1068 GLN E 92 GLN H 76 ASN ** M 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 144 GLN ** O 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 45231 Z= 0.302 Angle : 0.556 15.727 61434 Z= 0.287 Chirality : 0.043 0.229 6849 Planarity : 0.004 0.049 7660 Dihedral : 12.210 59.970 6736 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.63 % Allowed : 11.68 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.12), residues: 5233 helix: 1.29 (0.12), residues: 1976 sheet: 0.61 (0.18), residues: 827 loop : 0.09 (0.13), residues: 2430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 27 HIS 0.015 0.001 HIS M 18 PHE 0.024 0.002 PHE A 592 TYR 0.025 0.002 TYR G 3 ARG 0.010 0.001 ARG R 51 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10466 Ramachandran restraints generated. 5233 Oldfield, 0 Emsley, 5233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10466 Ramachandran restraints generated. 5233 Oldfield, 0 Emsley, 5233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 745 residues out of total 4684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 622 time to evaluate : 4.993 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: A 16 ARG cc_start: 0.7843 (mmt90) cc_final: 0.7614 (mpt-90) REVERT: A 67 ARG cc_start: 0.7690 (mmm160) cc_final: 0.7073 (mmm160) REVERT: A 220 ARG cc_start: 0.8221 (tpt-90) cc_final: 0.7812 (tpm-80) REVERT: A 296 ASN cc_start: 0.7697 (m-40) cc_final: 0.7468 (m110) REVERT: A 423 ASN cc_start: 0.7614 (p0) cc_final: 0.7163 (p0) REVERT: A 439 HIS cc_start: 0.7392 (t70) cc_final: 0.7089 (m-70) REVERT: A 1071 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7487 (tm-30) REVERT: A 1155 LYS cc_start: 0.8017 (ttpt) cc_final: 0.7558 (tttm) REVERT: A 1306 LYS cc_start: 0.8038 (ttmm) cc_final: 0.7800 (tppt) REVERT: A 1472 ASP cc_start: 0.7705 (m-30) cc_final: 0.7491 (m-30) REVERT: B 287 HIS cc_start: 0.8428 (m90) cc_final: 0.8110 (m90) REVERT: B 677 MET cc_start: 0.9036 (tpp) cc_final: 0.8752 (tpt) REVERT: B 731 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7829 (mt0) REVERT: B 995 GLU cc_start: 0.6894 (OUTLIER) cc_final: 0.6687 (tm-30) REVERT: C 17 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7141 (mt-10) REVERT: C 86 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7526 (ptt90) REVERT: C 111 GLN cc_start: 0.6864 (OUTLIER) cc_final: 0.6376 (mm-40) REVERT: E 116 GLN cc_start: 0.8336 (tp40) cc_final: 0.8136 (tp40) REVERT: E 131 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8423 (mm) REVERT: F 59 LYS cc_start: 0.9125 (ptpt) cc_final: 0.8820 (ptmt) REVERT: G 117 MET cc_start: -0.0602 (mmm) cc_final: -0.1039 (tmm) REVERT: H 103 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7252 (pm20) REVERT: H 111 ARG cc_start: 0.8035 (mmm-85) cc_final: 0.7645 (mtp-110) REVERT: H 123 MET cc_start: 0.9005 (ttp) cc_final: 0.8765 (ttp) REVERT: H 147 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8213 (ttmm) REVERT: I 45 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.8136 (mt0) REVERT: I 56 ASN cc_start: 0.8785 (t0) cc_final: 0.8322 (t0) REVERT: J 1 MET cc_start: 0.7922 (OUTLIER) cc_final: 0.7712 (mtp) REVERT: M 52 TRP cc_start: 0.8342 (p90) cc_final: 0.8023 (p90) REVERT: M 86 LYS cc_start: 0.7841 (mttt) cc_final: 0.7379 (mptt) REVERT: M 190 GLU cc_start: 0.7396 (tp30) cc_final: 0.7089 (tp30) REVERT: M 227 GLN cc_start: 0.7315 (pm20) cc_final: 0.7014 (pm20) REVERT: M 300 PHE cc_start: 0.8060 (m-80) cc_final: 0.7783 (m-80) REVERT: O 167 ASN cc_start: 0.8138 (OUTLIER) cc_final: 0.7929 (t0) REVERT: O 328 ILE cc_start: 0.9030 (OUTLIER) cc_final: 0.8718 (tp) REVERT: R 145 LEU cc_start: 0.7803 (mm) cc_final: 0.7439 (tp) REVERT: R 181 GLN cc_start: 0.7013 (tp-100) cc_final: 0.6724 (tp-100) outliers start: 123 outliers final: 53 residues processed: 687 average time/residue: 1.8561 time to fit residues: 1538.8805 Evaluate side-chains 668 residues out of total 4684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 602 time to evaluate : 4.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 1052 ARG Chi-restraints excluded: chain A residue 1071 GLU Chi-restraints excluded: chain A residue 1147 SER Chi-restraints excluded: chain A residue 1164 THR Chi-restraints excluded: chain A residue 1351 ASP Chi-restraints excluded: chain A residue 1441 GLU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 503 ASN Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 731 GLN Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 828 VAL Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 892 CYS Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 995 GLU Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 41 LYS Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain H residue 55 LYS Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 103 GLU Chi-restraints excluded: chain H residue 128 ASP Chi-restraints excluded: chain H residue 147 LYS Chi-restraints excluded: chain I residue 45 GLN Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain M residue 96 PHE Chi-restraints excluded: chain M residue 282 ASP Chi-restraints excluded: chain O residue 167 ASN Chi-restraints excluded: chain O residue 328 ILE Chi-restraints excluded: chain Q residue 177 MET Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 211 VAL Chi-restraints excluded: chain W residue 34 LEU Chi-restraints excluded: chain W residue 48 MET Chi-restraints excluded: chain W residue 66 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 526 random chunks: chunk 472 optimal weight: 9.9990 chunk 359 optimal weight: 0.5980 chunk 248 optimal weight: 0.3980 chunk 52 optimal weight: 1.9990 chunk 228 optimal weight: 0.5980 chunk 321 optimal weight: 2.9990 chunk 480 optimal weight: 8.9990 chunk 508 optimal weight: 0.6980 chunk 250 optimal weight: 2.9990 chunk 455 optimal weight: 9.9990 chunk 137 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 459 ASN A 861 GLN ** A1194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1299 GLN A1310 HIS B 552 ASN B 968 ASN B1117 HIS C 18 ASN E 210 GLN G 24 ASN H 76 ASN ** M 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 263 GLN ** O 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 256 GLN R 144 GLN X 188 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 45231 Z= 0.191 Angle : 0.508 12.268 61434 Z= 0.262 Chirality : 0.041 0.203 6849 Planarity : 0.004 0.046 7660 Dihedral : 12.211 59.945 6734 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.58 % Allowed : 13.00 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.12), residues: 5233 helix: 1.40 (0.12), residues: 1974 sheet: 0.62 (0.18), residues: 831 loop : 0.07 (0.13), residues: 2428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 27 HIS 0.010 0.001 HIS M 18 PHE 0.023 0.001 PHE A 112 TYR 0.018 0.001 TYR B 160 ARG 0.010 0.000 ARG L 37 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10466 Ramachandran restraints generated. 5233 Oldfield, 0 Emsley, 5233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10466 Ramachandran restraints generated. 5233 Oldfield, 0 Emsley, 5233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 752 residues out of total 4684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 631 time to evaluate : 4.598 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 16 ARG cc_start: 0.7821 (mmt90) cc_final: 0.7571 (mpt-90) REVERT: A 67 ARG cc_start: 0.7695 (mmm160) cc_final: 0.7328 (mtp180) REVERT: A 220 ARG cc_start: 0.8136 (tpt-90) cc_final: 0.7702 (tpm-80) REVERT: A 226 LYS cc_start: 0.8181 (mtpt) cc_final: 0.7920 (mtpt) REVERT: A 296 ASN cc_start: 0.7673 (m-40) cc_final: 0.7401 (m110) REVERT: A 439 HIS cc_start: 0.7371 (t70) cc_final: 0.7090 (m-70) REVERT: A 1071 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7368 (tm-30) REVERT: A 1144 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8274 (tp) REVERT: A 1155 LYS cc_start: 0.7983 (ttpt) cc_final: 0.7524 (tttm) REVERT: A 1288 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8854 (mp) REVERT: A 1472 ASP cc_start: 0.7677 (m-30) cc_final: 0.7444 (m-30) REVERT: B 287 HIS cc_start: 0.8380 (m90) cc_final: 0.8088 (m90) REVERT: B 324 ARG cc_start: 0.8449 (mpt-90) cc_final: 0.8230 (mtt90) REVERT: B 677 MET cc_start: 0.9054 (tpp) cc_final: 0.8703 (tpt) REVERT: B 731 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7815 (mt0) REVERT: B 995 GLU cc_start: 0.6772 (OUTLIER) cc_final: 0.6569 (tm-30) REVERT: C 17 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7076 (mt-10) REVERT: C 20 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.8557 (tttm) REVERT: C 86 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7555 (ptt90) REVERT: C 111 GLN cc_start: 0.6803 (OUTLIER) cc_final: 0.6339 (mm-40) REVERT: E 116 GLN cc_start: 0.8251 (tp40) cc_final: 0.7879 (tp40) REVERT: E 131 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8454 (mm) REVERT: F 59 LYS cc_start: 0.9080 (ptpt) cc_final: 0.8749 (ptmt) REVERT: G 117 MET cc_start: -0.0437 (mmm) cc_final: -0.0869 (tmm) REVERT: H 103 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7230 (pm20) REVERT: H 111 ARG cc_start: 0.8084 (mmm-85) cc_final: 0.7693 (mtp-110) REVERT: H 123 MET cc_start: 0.8938 (ttp) cc_final: 0.8717 (ttp) REVERT: H 147 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8141 (ttmm) REVERT: I 56 ASN cc_start: 0.8793 (t0) cc_final: 0.8330 (t0) REVERT: L 47 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7890 (ptmm) REVERT: M 52 TRP cc_start: 0.8315 (p90) cc_final: 0.7989 (p90) REVERT: M 86 LYS cc_start: 0.7839 (mttt) cc_final: 0.7369 (mptt) REVERT: M 124 MET cc_start: 0.8788 (mtm) cc_final: 0.8389 (mtp) REVERT: M 190 GLU cc_start: 0.7340 (tp30) cc_final: 0.7055 (tp30) REVERT: M 227 GLN cc_start: 0.7359 (pm20) cc_final: 0.7049 (pm20) REVERT: M 300 PHE cc_start: 0.8031 (m-80) cc_final: 0.7703 (m-80) REVERT: M 303 ASP cc_start: 0.7430 (OUTLIER) cc_final: 0.6911 (p0) REVERT: R 122 GLU cc_start: 0.3246 (mm-30) cc_final: 0.2429 (mm-30) REVERT: W 76 MET cc_start: 0.2555 (mmm) cc_final: 0.2250 (mmp) outliers start: 121 outliers final: 47 residues processed: 692 average time/residue: 1.8322 time to fit residues: 1527.5468 Evaluate side-chains 665 residues out of total 4684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 604 time to evaluate : 5.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 1052 ARG Chi-restraints excluded: chain A residue 1071 GLU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1147 SER Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1339 ASP Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1351 ASP Chi-restraints excluded: chain A residue 1441 GLU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 503 ASN Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 731 GLN Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 919 CYS Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 995 GLU Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 41 LYS Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain G residue 77 PHE Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain H residue 55 LYS Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 103 GLU Chi-restraints excluded: chain H residue 130 ASN Chi-restraints excluded: chain H residue 147 LYS Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain L residue 47 LYS Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain M residue 96 PHE Chi-restraints excluded: chain M residue 282 ASP Chi-restraints excluded: chain M residue 303 ASP Chi-restraints excluded: chain Q residue 177 MET Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 144 GLN Chi-restraints excluded: chain R residue 211 VAL Chi-restraints excluded: chain W residue 66 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 526 random chunks: chunk 423 optimal weight: 0.6980 chunk 288 optimal weight: 40.0000 chunk 7 optimal weight: 0.9990 chunk 378 optimal weight: 0.9990 chunk 209 optimal weight: 0.8980 chunk 433 optimal weight: 30.0000 chunk 351 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 259 optimal weight: 0.6980 chunk 456 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 861 GLN ** A1194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1236 ASN ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 552 ASN H 76 ASN M 263 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 45231 Z= 0.246 Angle : 0.525 11.806 61434 Z= 0.269 Chirality : 0.042 0.207 6849 Planarity : 0.004 0.052 7660 Dihedral : 12.245 59.781 6734 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.56 % Allowed : 14.09 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.12), residues: 5233 helix: 1.38 (0.12), residues: 1977 sheet: 0.57 (0.18), residues: 835 loop : 0.05 (0.13), residues: 2421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 27 HIS 0.012 0.001 HIS M 18 PHE 0.028 0.002 PHE G 107 TYR 0.036 0.001 TYR B 160 ARG 0.012 0.000 ARG R 51 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10466 Ramachandran restraints generated. 5233 Oldfield, 0 Emsley, 5233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10466 Ramachandran restraints generated. 5233 Oldfield, 0 Emsley, 5233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 728 residues out of total 4684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 608 time to evaluate : 5.058 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 16 ARG cc_start: 0.7827 (mmt90) cc_final: 0.7575 (mpt-90) REVERT: A 67 ARG cc_start: 0.7704 (mmm160) cc_final: 0.7104 (mmm160) REVERT: A 220 ARG cc_start: 0.8188 (tpt-90) cc_final: 0.7737 (tpm-80) REVERT: A 296 ASN cc_start: 0.7732 (m-40) cc_final: 0.7426 (m110) REVERT: A 425 ASP cc_start: 0.7642 (m-30) cc_final: 0.7383 (m-30) REVERT: A 439 HIS cc_start: 0.7386 (t70) cc_final: 0.7092 (m-70) REVERT: A 1071 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7394 (tm-30) REVERT: A 1155 LYS cc_start: 0.7989 (ttpt) cc_final: 0.7523 (tttm) REVERT: A 1288 ILE cc_start: 0.9046 (OUTLIER) cc_final: 0.8820 (mp) REVERT: A 1472 ASP cc_start: 0.7685 (m-30) cc_final: 0.7447 (m-30) REVERT: B 287 HIS cc_start: 0.8372 (m90) cc_final: 0.8081 (m90) REVERT: B 324 ARG cc_start: 0.8389 (mpt-90) cc_final: 0.8161 (mtt90) REVERT: B 677 MET cc_start: 0.9034 (tpp) cc_final: 0.8753 (tpt) REVERT: B 731 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.7810 (mt0) REVERT: C 17 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7132 (mt-10) REVERT: C 20 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8589 (tttm) REVERT: C 41 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7317 (mp0) REVERT: C 86 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7611 (ptt90) REVERT: C 111 GLN cc_start: 0.6768 (OUTLIER) cc_final: 0.6321 (mm-40) REVERT: C 254 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7944 (ttmt) REVERT: E 116 GLN cc_start: 0.8228 (tp40) cc_final: 0.7850 (tp40) REVERT: E 131 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8477 (mm) REVERT: E 210 GLN cc_start: 0.6482 (OUTLIER) cc_final: 0.6236 (tt0) REVERT: F 59 LYS cc_start: 0.9094 (ptpt) cc_final: 0.8757 (ptmt) REVERT: G 2 PHE cc_start: 0.6072 (m-10) cc_final: 0.5870 (m-10) REVERT: G 117 MET cc_start: -0.0541 (mmm) cc_final: -0.0985 (tmm) REVERT: H 103 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7197 (pm20) REVERT: H 111 ARG cc_start: 0.8076 (mmm-85) cc_final: 0.7678 (mtp-110) REVERT: H 123 MET cc_start: 0.8968 (ttp) cc_final: 0.8726 (ttp) REVERT: H 147 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8115 (ttmm) REVERT: I 56 ASN cc_start: 0.8825 (t0) cc_final: 0.8372 (t0) REVERT: L 47 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.8006 (ptmm) REVERT: M 52 TRP cc_start: 0.8325 (p90) cc_final: 0.8007 (p90) REVERT: M 86 LYS cc_start: 0.7738 (mttt) cc_final: 0.7307 (mptt) REVERT: M 124 MET cc_start: 0.8804 (mtm) cc_final: 0.8423 (mtp) REVERT: M 190 GLU cc_start: 0.7376 (tp30) cc_final: 0.7098 (tp30) REVERT: M 227 GLN cc_start: 0.7366 (pm20) cc_final: 0.7059 (pm20) REVERT: R 145 LEU cc_start: 0.7834 (mm) cc_final: 0.7403 (tp) outliers start: 120 outliers final: 61 residues processed: 671 average time/residue: 1.7596 time to fit residues: 1429.1909 Evaluate side-chains 669 residues out of total 4684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 594 time to evaluate : 5.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 1071 GLU Chi-restraints excluded: chain A residue 1147 SER Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1309 MET Chi-restraints excluded: chain A residue 1338 THR Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1351 ASP Chi-restraints excluded: chain A residue 1398 LEU Chi-restraints excluded: chain A residue 1437 ASP Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 503 ASN Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 731 GLN Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 828 VAL Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain B residue 919 CYS Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 41 LYS Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 140 THR Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain G residue 44 PHE Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain H residue 55 LYS Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 103 GLU Chi-restraints excluded: chain H residue 130 ASN Chi-restraints excluded: chain H residue 147 LYS Chi-restraints excluded: chain I residue 27 LYS Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain L residue 47 LYS Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain M residue 96 PHE Chi-restraints excluded: chain M residue 282 ASP Chi-restraints excluded: chain M residue 303 ASP Chi-restraints excluded: chain O residue 328 ILE Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 211 VAL Chi-restraints excluded: chain W residue 66 LEU Chi-restraints excluded: chain W residue 115 GLU Chi-restraints excluded: chain W residue 164 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 526 random chunks: chunk 171 optimal weight: 3.9990 chunk 457 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 298 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 508 optimal weight: 20.0000 chunk 422 optimal weight: 10.0000 chunk 235 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 267 optimal weight: 0.2980 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 861 GLN ** A1194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 552 ASN H 76 ASN M 263 GLN Q 121 ASN R 144 GLN V 27 GLN W 101 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 45231 Z= 0.395 Angle : 0.595 11.876 61434 Z= 0.304 Chirality : 0.045 0.240 6849 Planarity : 0.005 0.062 7660 Dihedral : 12.400 59.932 6734 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.60 % Allowed : 14.52 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.12), residues: 5233 helix: 1.19 (0.12), residues: 1973 sheet: 0.48 (0.18), residues: 818 loop : -0.04 (0.13), residues: 2442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 203 HIS 0.013 0.001 HIS M 18 PHE 0.029 0.002 PHE A 592 TYR 0.024 0.002 TYR B 160 ARG 0.013 0.001 ARG R 51 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10466 Ramachandran restraints generated. 5233 Oldfield, 0 Emsley, 5233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10466 Ramachandran restraints generated. 5233 Oldfield, 0 Emsley, 5233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 726 residues out of total 4684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 604 time to evaluate : 5.236 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 16 ARG cc_start: 0.7847 (mmt90) cc_final: 0.7617 (mpt-90) REVERT: A 67 ARG cc_start: 0.7739 (mmm160) cc_final: 0.7117 (mmm160) REVERT: A 220 ARG cc_start: 0.8206 (tpt-90) cc_final: 0.7704 (tpm-80) REVERT: A 239 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.6962 (tm-30) REVERT: A 296 ASN cc_start: 0.7705 (m-40) cc_final: 0.7406 (m110) REVERT: A 439 HIS cc_start: 0.7405 (t70) cc_final: 0.7112 (m-70) REVERT: A 1052 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.6360 (tpp-160) REVERT: A 1071 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7471 (tm-30) REVERT: A 1155 LYS cc_start: 0.8033 (ttpt) cc_final: 0.7571 (tttm) REVERT: A 1288 ILE cc_start: 0.9059 (OUTLIER) cc_final: 0.8823 (mp) REVERT: A 1472 ASP cc_start: 0.7715 (m-30) cc_final: 0.7475 (m-30) REVERT: B 287 HIS cc_start: 0.8433 (m90) cc_final: 0.8103 (m90) REVERT: B 324 ARG cc_start: 0.8424 (mpt-90) cc_final: 0.8200 (mtt90) REVERT: B 425 ARG cc_start: 0.7452 (mtm110) cc_final: 0.7143 (mtp180) REVERT: B 731 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.7870 (mt0) REVERT: C 17 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7143 (mt-10) REVERT: C 41 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7349 (mp0) REVERT: C 111 GLN cc_start: 0.6931 (OUTLIER) cc_final: 0.6464 (mm-40) REVERT: C 205 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8293 (mptm) REVERT: E 131 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8547 (mm) REVERT: G 117 MET cc_start: -0.0485 (mmm) cc_final: -0.0716 (tmm) REVERT: H 103 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7234 (pm20) REVERT: H 111 ARG cc_start: 0.8049 (mmm-85) cc_final: 0.7768 (mtp-110) REVERT: H 123 MET cc_start: 0.9024 (ttp) cc_final: 0.8774 (ttp) REVERT: H 147 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8199 (ttmm) REVERT: I 56 ASN cc_start: 0.8869 (t0) cc_final: 0.8446 (t0) REVERT: M 52 TRP cc_start: 0.8344 (p90) cc_final: 0.7983 (p90) REVERT: M 86 LYS cc_start: 0.7729 (mttt) cc_final: 0.7310 (mptt) REVERT: M 227 GLN cc_start: 0.7377 (pm20) cc_final: 0.7101 (pm20) REVERT: R 181 GLN cc_start: 0.7028 (tp-100) cc_final: 0.6780 (tp-100) REVERT: W 48 MET cc_start: 0.3577 (mtt) cc_final: 0.2755 (mmt) outliers start: 122 outliers final: 67 residues processed: 667 average time/residue: 1.8087 time to fit residues: 1459.3778 Evaluate side-chains 675 residues out of total 4684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 596 time to evaluate : 4.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 239 GLU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 1052 ARG Chi-restraints excluded: chain A residue 1071 GLU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1147 SER Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1338 THR Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1351 ASP Chi-restraints excluded: chain A residue 1437 ASP Chi-restraints excluded: chain A residue 1441 GLU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 503 ASN Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 731 GLN Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 828 VAL Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 892 CYS Chi-restraints excluded: chain B residue 919 CYS Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 205 LYS Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 41 LYS Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 55 LYS Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 103 GLU Chi-restraints excluded: chain H residue 130 ASN Chi-restraints excluded: chain H residue 147 LYS Chi-restraints excluded: chain I residue 27 LYS Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 282 ASP Chi-restraints excluded: chain M residue 303 ASP Chi-restraints excluded: chain O residue 328 ILE Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 144 GLN Chi-restraints excluded: chain R residue 211 VAL Chi-restraints excluded: chain W residue 66 LEU Chi-restraints excluded: chain W residue 164 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 526 random chunks: chunk 490 optimal weight: 50.0000 chunk 57 optimal weight: 0.8980 chunk 289 optimal weight: 30.0000 chunk 371 optimal weight: 0.0770 chunk 287 optimal weight: 6.9990 chunk 428 optimal weight: 0.9990 chunk 284 optimal weight: 5.9990 chunk 506 optimal weight: 0.0980 chunk 317 optimal weight: 0.6980 chunk 309 optimal weight: 0.8980 chunk 234 optimal weight: 0.5980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 861 GLN ** A1194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1236 ASN B 111 ASN ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 420 GLN B 552 ASN B 582 GLN B 585 ASN C 18 ASN E 210 GLN H 76 ASN M 263 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 45231 Z= 0.186 Angle : 0.512 12.700 61434 Z= 0.261 Chirality : 0.041 0.212 6849 Planarity : 0.004 0.067 7660 Dihedral : 12.300 59.726 6734 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.26 % Allowed : 15.39 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.12), residues: 5233 helix: 1.37 (0.12), residues: 1977 sheet: 0.50 (0.18), residues: 815 loop : -0.02 (0.13), residues: 2441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 203 HIS 0.011 0.001 HIS M 18 PHE 0.021 0.001 PHE A 397 TYR 0.020 0.001 TYR B 160 ARG 0.015 0.000 ARG R 51 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10466 Ramachandran restraints generated. 5233 Oldfield, 0 Emsley, 5233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10466 Ramachandran restraints generated. 5233 Oldfield, 0 Emsley, 5233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 717 residues out of total 4684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 611 time to evaluate : 5.401 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: A 16 ARG cc_start: 0.7825 (mmt90) cc_final: 0.7582 (mpt-90) REVERT: A 67 ARG cc_start: 0.7764 (mmm160) cc_final: 0.7391 (mtp180) REVERT: A 220 ARG cc_start: 0.8195 (tpt-90) cc_final: 0.7734 (tpm-80) REVERT: A 296 ASN cc_start: 0.7745 (m-40) cc_final: 0.7481 (m110) REVERT: A 439 HIS cc_start: 0.7386 (t70) cc_final: 0.7092 (m-70) REVERT: A 1071 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7378 (tm-30) REVERT: A 1155 LYS cc_start: 0.8016 (ttpt) cc_final: 0.7547 (tttm) REVERT: A 1288 ILE cc_start: 0.9021 (OUTLIER) cc_final: 0.8770 (mp) REVERT: A 1472 ASP cc_start: 0.7669 (m-30) cc_final: 0.7417 (m-30) REVERT: B 287 HIS cc_start: 0.8423 (m90) cc_final: 0.8130 (m90) REVERT: B 324 ARG cc_start: 0.8374 (mpt-90) cc_final: 0.8128 (mtt90) REVERT: B 425 ARG cc_start: 0.7385 (mtm110) cc_final: 0.7138 (mtp180) REVERT: B 603 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.8324 (mtm) REVERT: B 677 MET cc_start: 0.9043 (tpp) cc_final: 0.8759 (tpt) REVERT: B 731 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7805 (mt0) REVERT: C 17 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7027 (mt-10) REVERT: C 86 ARG cc_start: 0.8169 (OUTLIER) cc_final: 0.7549 (ptt90) REVERT: C 111 GLN cc_start: 0.6862 (OUTLIER) cc_final: 0.6400 (mm-40) REVERT: E 41 LYS cc_start: 0.8388 (OUTLIER) cc_final: 0.7775 (mmtt) REVERT: E 116 GLN cc_start: 0.8351 (tp40) cc_final: 0.7850 (tp40) REVERT: E 126 ILE cc_start: 0.9217 (mm) cc_final: 0.8963 (mm) REVERT: E 131 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8468 (mm) REVERT: F 59 LYS cc_start: 0.9079 (ptpt) cc_final: 0.8741 (ptmt) REVERT: G 117 MET cc_start: -0.0511 (mmm) cc_final: -0.0763 (tmm) REVERT: H 111 ARG cc_start: 0.8043 (mmm-85) cc_final: 0.7773 (mtp-110) REVERT: H 123 MET cc_start: 0.8941 (ttp) cc_final: 0.8702 (ttp) REVERT: H 147 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8123 (ttmm) REVERT: I 56 ASN cc_start: 0.8888 (t0) cc_final: 0.8447 (t0) REVERT: M 52 TRP cc_start: 0.8319 (p90) cc_final: 0.8015 (p90) REVERT: M 86 LYS cc_start: 0.7661 (mttt) cc_final: 0.7274 (mptt) REVERT: M 190 GLU cc_start: 0.7348 (tp30) cc_final: 0.7091 (tp30) REVERT: M 227 GLN cc_start: 0.7345 (pm20) cc_final: 0.7037 (pm20) REVERT: O 229 GLN cc_start: 0.8191 (mm-40) cc_final: 0.7630 (tp-100) REVERT: V 90 VAL cc_start: -0.2157 (OUTLIER) cc_final: -0.2663 (t) REVERT: W 48 MET cc_start: 0.3669 (mtt) cc_final: 0.2884 (mmt) outliers start: 106 outliers final: 57 residues processed: 670 average time/residue: 1.8730 time to fit residues: 1514.6319 Evaluate side-chains 661 residues out of total 4684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 593 time to evaluate : 4.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 1052 ARG Chi-restraints excluded: chain A residue 1071 GLU Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1351 ASP Chi-restraints excluded: chain A residue 1437 ASP Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 503 ASN Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 603 MET Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 731 GLN Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 871 VAL Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 41 LYS Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain H residue 55 LYS Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 147 LYS Chi-restraints excluded: chain I residue 27 LYS Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain J residue 49 LEU Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain M residue 96 PHE Chi-restraints excluded: chain M residue 282 ASP Chi-restraints excluded: chain O residue 328 ILE Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 211 VAL Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain W residue 66 LEU Chi-restraints excluded: chain W residue 115 GLU Chi-restraints excluded: chain W residue 146 ASP Chi-restraints excluded: chain W residue 164 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 526 random chunks: chunk 313 optimal weight: 0.9980 chunk 202 optimal weight: 3.9990 chunk 302 optimal weight: 0.9990 chunk 152 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 322 optimal weight: 3.9990 chunk 345 optimal weight: 1.9990 chunk 250 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 398 optimal weight: 4.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 ASN A 576 GLN A 861 GLN ** A1194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1251 ASN A1422 GLN B 111 ASN H 76 ASN I 22 ASN K 69 HIS K 89 ASN ** M 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 263 GLN R 144 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 45231 Z= 0.334 Angle : 0.576 13.378 61434 Z= 0.292 Chirality : 0.044 0.223 6849 Planarity : 0.004 0.070 7660 Dihedral : 12.383 59.974 6734 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.26 % Allowed : 15.82 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.12), residues: 5233 helix: 1.26 (0.12), residues: 1971 sheet: 0.51 (0.18), residues: 816 loop : -0.06 (0.13), residues: 2446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 27 HIS 0.013 0.001 HIS M 18 PHE 0.026 0.002 PHE A 592 TYR 0.023 0.002 TYR B 160 ARG 0.017 0.001 ARG R 51 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10466 Ramachandran restraints generated. 5233 Oldfield, 0 Emsley, 5233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10466 Ramachandran restraints generated. 5233 Oldfield, 0 Emsley, 5233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 4684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 600 time to evaluate : 4.551 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 16 ARG cc_start: 0.7842 (mmt90) cc_final: 0.7618 (mpt-90) REVERT: A 67 ARG cc_start: 0.7739 (mmm160) cc_final: 0.7386 (mtp180) REVERT: A 220 ARG cc_start: 0.8192 (tpt-90) cc_final: 0.7710 (tpm-80) REVERT: A 296 ASN cc_start: 0.7634 (m-40) cc_final: 0.7363 (m110) REVERT: A 439 HIS cc_start: 0.7395 (t70) cc_final: 0.7098 (m-70) REVERT: A 1052 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.6354 (tpp-160) REVERT: A 1071 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7414 (tm-30) REVERT: A 1155 LYS cc_start: 0.8022 (ttpt) cc_final: 0.7547 (tttm) REVERT: A 1288 ILE cc_start: 0.9031 (OUTLIER) cc_final: 0.8777 (mp) REVERT: A 1412 MET cc_start: 0.8642 (ttp) cc_final: 0.8326 (ttp) REVERT: A 1472 ASP cc_start: 0.7740 (m-30) cc_final: 0.7490 (m-30) REVERT: B 287 HIS cc_start: 0.8480 (m90) cc_final: 0.8198 (m90) REVERT: B 324 ARG cc_start: 0.8435 (mpt-90) cc_final: 0.8229 (mtt90) REVERT: B 425 ARG cc_start: 0.7492 (mtm110) cc_final: 0.7095 (mtp180) REVERT: B 731 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.7866 (mt0) REVERT: C 17 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7146 (mt-10) REVERT: C 41 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7371 (mp0) REVERT: C 86 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7571 (ptt90) REVERT: C 111 GLN cc_start: 0.6914 (OUTLIER) cc_final: 0.6439 (mm-40) REVERT: E 131 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8531 (mm) REVERT: E 210 GLN cc_start: 0.6456 (OUTLIER) cc_final: 0.6251 (tt0) REVERT: G 46 ILE cc_start: 0.7773 (mp) cc_final: 0.7091 (mp) REVERT: G 117 MET cc_start: -0.0461 (mmm) cc_final: -0.0719 (tmm) REVERT: H 103 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7246 (pm20) REVERT: H 111 ARG cc_start: 0.8042 (mmm-85) cc_final: 0.7775 (mtp-110) REVERT: H 123 MET cc_start: 0.8996 (ttp) cc_final: 0.8748 (ttp) REVERT: H 147 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8198 (ttmm) REVERT: I 56 ASN cc_start: 0.8912 (t0) cc_final: 0.8462 (t0) REVERT: M 52 TRP cc_start: 0.8351 (p90) cc_final: 0.7991 (p90) REVERT: M 86 LYS cc_start: 0.7716 (mttt) cc_final: 0.7282 (mptt) REVERT: M 124 MET cc_start: 0.8774 (mtm) cc_final: 0.8406 (mtp) REVERT: M 227 GLN cc_start: 0.7353 (pm20) cc_final: 0.7098 (pm20) REVERT: O 229 GLN cc_start: 0.8247 (mm-40) cc_final: 0.7816 (tp-100) REVERT: U 358 MET cc_start: 0.4928 (ppp) cc_final: 0.3954 (pmm) REVERT: V 90 VAL cc_start: -0.2163 (OUTLIER) cc_final: -0.2673 (t) REVERT: W 48 MET cc_start: 0.3668 (mtt) cc_final: 0.2893 (mmt) outliers start: 106 outliers final: 66 residues processed: 661 average time/residue: 1.8075 time to fit residues: 1445.4443 Evaluate side-chains 662 residues out of total 4684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 583 time to evaluate : 4.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 715 GLU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 853 LYS Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 1052 ARG Chi-restraints excluded: chain A residue 1071 GLU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1147 SER Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1351 ASP Chi-restraints excluded: chain A residue 1437 ASP Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 300 MET Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 503 ASN Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 731 GLN Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 828 VAL Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 41 LYS Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 137 ILE Chi-restraints excluded: chain E residue 210 GLN Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain H residue 55 LYS Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 103 GLU Chi-restraints excluded: chain H residue 147 LYS Chi-restraints excluded: chain I residue 27 LYS Chi-restraints excluded: chain I residue 41 ASN Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain M residue 282 ASP Chi-restraints excluded: chain M residue 303 ASP Chi-restraints excluded: chain O residue 328 ILE Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 211 VAL Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain W residue 66 LEU Chi-restraints excluded: chain W residue 115 GLU Chi-restraints excluded: chain W residue 146 ASP Chi-restraints excluded: chain W residue 164 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 526 random chunks: chunk 461 optimal weight: 7.9990 chunk 485 optimal weight: 9.9990 chunk 443 optimal weight: 6.9990 chunk 472 optimal weight: 10.0000 chunk 284 optimal weight: 7.9990 chunk 205 optimal weight: 0.2980 chunk 370 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 chunk 426 optimal weight: 8.9990 chunk 446 optimal weight: 10.0000 chunk 470 optimal weight: 4.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 ASN A 861 GLN A1236 ASN B 111 ASN C 18 ASN H 76 ASN K 89 ASN M 263 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.111 45231 Z= 0.660 Angle : 0.728 13.749 61434 Z= 0.372 Chirality : 0.052 0.327 6849 Planarity : 0.006 0.103 7660 Dihedral : 12.650 59.913 6734 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.94 % Favored : 97.04 % Rotamer: Outliers : 2.41 % Allowed : 16.05 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.11), residues: 5233 helix: 0.82 (0.12), residues: 1975 sheet: 0.42 (0.18), residues: 797 loop : -0.24 (0.12), residues: 2461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP C 203 HIS 0.023 0.002 HIS M 18 PHE 0.039 0.003 PHE A 592 TYR 0.034 0.003 TYR B 160 ARG 0.017 0.001 ARG R 51 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10466 Ramachandran restraints generated. 5233 Oldfield, 0 Emsley, 5233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10466 Ramachandran restraints generated. 5233 Oldfield, 0 Emsley, 5233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 4684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 593 time to evaluate : 4.905 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 16 ARG cc_start: 0.7929 (mmt90) cc_final: 0.7675 (mpt-90) REVERT: A 220 ARG cc_start: 0.8289 (tpt-90) cc_final: 0.7876 (tpt170) REVERT: A 439 HIS cc_start: 0.7416 (t70) cc_final: 0.7120 (m-70) REVERT: A 743 ARG cc_start: 0.7681 (OUTLIER) cc_final: 0.7320 (ttp80) REVERT: A 1052 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.6427 (tpp-160) REVERT: A 1155 LYS cc_start: 0.8040 (ttpt) cc_final: 0.7578 (tttm) REVERT: A 1242 ASP cc_start: 0.6598 (t70) cc_final: 0.6360 (t0) REVERT: A 1288 ILE cc_start: 0.9053 (OUTLIER) cc_final: 0.8825 (mp) REVERT: A 1472 ASP cc_start: 0.7865 (m-30) cc_final: 0.7610 (m-30) REVERT: B 287 HIS cc_start: 0.8546 (m90) cc_final: 0.8246 (m90) REVERT: B 298 MET cc_start: 0.7931 (mtp) cc_final: 0.7707 (mtp) REVERT: B 324 ARG cc_start: 0.8522 (mpt-90) cc_final: 0.8255 (mtt90) REVERT: B 425 ARG cc_start: 0.7676 (mtm110) cc_final: 0.7140 (mtp180) REVERT: B 731 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.7974 (mt0) REVERT: B 1104 ARG cc_start: 0.8691 (ttt-90) cc_final: 0.8418 (ttp-170) REVERT: C 17 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7215 (mt-10) REVERT: C 41 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7368 (mp0) REVERT: C 111 GLN cc_start: 0.7007 (OUTLIER) cc_final: 0.6585 (mm-40) REVERT: E 131 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8622 (mm) REVERT: G 46 ILE cc_start: 0.7947 (mp) cc_final: 0.7256 (mp) REVERT: G 117 MET cc_start: -0.0243 (mmm) cc_final: -0.0635 (tmm) REVERT: H 103 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7400 (pm20) REVERT: H 111 ARG cc_start: 0.8105 (mmm-85) cc_final: 0.7769 (mtp-110) REVERT: H 123 MET cc_start: 0.9042 (ttp) cc_final: 0.8818 (ttp) REVERT: H 147 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8240 (ttmm) REVERT: I 109 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.8171 (ptp90) REVERT: J 58 LYS cc_start: 0.7949 (mmtt) cc_final: 0.7698 (tptt) REVERT: M 52 TRP cc_start: 0.8411 (p90) cc_final: 0.8148 (p90) REVERT: M 86 LYS cc_start: 0.7867 (mttt) cc_final: 0.7409 (mtpt) REVERT: M 227 GLN cc_start: 0.7236 (pm20) cc_final: 0.6897 (pm20) REVERT: O 229 GLN cc_start: 0.8281 (mm-40) cc_final: 0.7977 (tp-100) REVERT: R 181 GLN cc_start: 0.7094 (tp-100) cc_final: 0.6851 (tp-100) REVERT: U 358 MET cc_start: 0.5149 (ppp) cc_final: 0.4020 (pmm) REVERT: V 90 VAL cc_start: -0.2137 (OUTLIER) cc_final: -0.2649 (t) REVERT: W 48 MET cc_start: 0.3694 (mtt) cc_final: 0.2887 (mmt) REVERT: W 76 MET cc_start: 0.2077 (mmp) cc_final: 0.0937 (mmm) outliers start: 113 outliers final: 69 residues processed: 660 average time/residue: 1.8141 time to fit residues: 1455.1310 Evaluate side-chains 663 residues out of total 4684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 582 time to evaluate : 5.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 458 PHE Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 695 ASP Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 743 ARG Chi-restraints excluded: chain A residue 853 LYS Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 1052 ARG Chi-restraints excluded: chain A residue 1071 GLU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1147 SER Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1338 THR Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1351 ASP Chi-restraints excluded: chain A residue 1437 ASP Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 503 ASN Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 731 GLN Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 828 VAL Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 892 CYS Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 41 LYS Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain H residue 55 LYS Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 103 GLU Chi-restraints excluded: chain H residue 147 LYS Chi-restraints excluded: chain I residue 27 LYS Chi-restraints excluded: chain I residue 41 ASN Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 109 ARG Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 282 ASP Chi-restraints excluded: chain M residue 303 ASP Chi-restraints excluded: chain O residue 328 ILE Chi-restraints excluded: chain Q residue 156 THR Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 211 VAL Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain W residue 66 LEU Chi-restraints excluded: chain W residue 115 GLU Chi-restraints excluded: chain W residue 146 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 526 random chunks: chunk 310 optimal weight: 1.9990 chunk 499 optimal weight: 40.0000 chunk 304 optimal weight: 1.9990 chunk 236 optimal weight: 0.7980 chunk 347 optimal weight: 0.8980 chunk 524 optimal weight: 6.9990 chunk 482 optimal weight: 0.9990 chunk 417 optimal weight: 20.0000 chunk 43 optimal weight: 1.9990 chunk 322 optimal weight: 5.9990 chunk 255 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 ASN A 296 ASN A 861 GLN B 500 GLN B 585 ASN H 76 ASN I 22 ASN K 89 ASN M 263 GLN V 39 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 45231 Z= 0.294 Angle : 0.588 14.779 61434 Z= 0.297 Chirality : 0.043 0.228 6849 Planarity : 0.004 0.082 7660 Dihedral : 12.530 59.769 6734 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.88 % Allowed : 16.78 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.12), residues: 5233 helix: 1.09 (0.12), residues: 1964 sheet: 0.38 (0.18), residues: 811 loop : -0.16 (0.13), residues: 2458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 479 HIS 0.015 0.001 HIS M 18 PHE 0.026 0.002 PHE A 112 TYR 0.023 0.002 TYR E 90 ARG 0.019 0.001 ARG R 51 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10466 Ramachandran restraints generated. 5233 Oldfield, 0 Emsley, 5233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10466 Ramachandran restraints generated. 5233 Oldfield, 0 Emsley, 5233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 4684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 586 time to evaluate : 5.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 16 ARG cc_start: 0.7867 (mmt90) cc_final: 0.7617 (mpt-90) REVERT: A 58 MET cc_start: 0.7846 (mmp) cc_final: 0.7554 (mmt) REVERT: A 67 ARG cc_start: 0.7750 (mmm160) cc_final: 0.7199 (mmm160) REVERT: A 220 ARG cc_start: 0.8250 (tpt-90) cc_final: 0.7781 (tpm-80) REVERT: A 439 HIS cc_start: 0.7390 (t70) cc_final: 0.7090 (m-70) REVERT: A 1052 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.6389 (tpp-160) REVERT: A 1071 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7474 (tm-30) REVERT: A 1155 LYS cc_start: 0.7988 (ttpt) cc_final: 0.7511 (tttm) REVERT: A 1242 ASP cc_start: 0.6511 (t70) cc_final: 0.6291 (t0) REVERT: A 1288 ILE cc_start: 0.9047 (OUTLIER) cc_final: 0.8787 (mp) REVERT: A 1472 ASP cc_start: 0.7803 (m-30) cc_final: 0.7589 (m-30) REVERT: B 287 HIS cc_start: 0.8490 (m90) cc_final: 0.8184 (m90) REVERT: B 324 ARG cc_start: 0.8438 (mpt-90) cc_final: 0.8216 (mtt90) REVERT: B 425 ARG cc_start: 0.7544 (mtm110) cc_final: 0.7147 (mtp180) REVERT: B 677 MET cc_start: 0.9074 (tpp) cc_final: 0.8789 (tpt) REVERT: B 731 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7848 (mt0) REVERT: C 17 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7209 (mt-10) REVERT: C 41 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7364 (mp0) REVERT: C 111 GLN cc_start: 0.6888 (OUTLIER) cc_final: 0.6411 (mm-40) REVERT: E 92 GLN cc_start: 0.7665 (tp-100) cc_final: 0.7441 (tp-100) REVERT: F 59 LYS cc_start: 0.9126 (ptpt) cc_final: 0.8808 (ptmt) REVERT: G 46 ILE cc_start: 0.7881 (mp) cc_final: 0.7321 (mp) REVERT: G 117 MET cc_start: -0.0236 (mmm) cc_final: -0.0597 (tmm) REVERT: H 103 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7298 (pm20) REVERT: H 111 ARG cc_start: 0.8111 (mmm-85) cc_final: 0.7871 (mtp-110) REVERT: H 123 MET cc_start: 0.8972 (ttp) cc_final: 0.8747 (ttp) REVERT: H 147 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8211 (ttmm) REVERT: J 58 LYS cc_start: 0.7894 (mmtt) cc_final: 0.7691 (tptt) REVERT: M 52 TRP cc_start: 0.8369 (p90) cc_final: 0.8044 (p90) REVERT: M 86 LYS cc_start: 0.7675 (mttt) cc_final: 0.7313 (mptt) REVERT: M 124 MET cc_start: 0.8713 (mtm) cc_final: 0.8412 (mtp) REVERT: M 227 GLN cc_start: 0.7301 (pm20) cc_final: 0.7041 (pm20) REVERT: O 229 GLN cc_start: 0.8251 (mm-40) cc_final: 0.7979 (tp-100) REVERT: R 181 GLN cc_start: 0.7075 (tp-100) cc_final: 0.6847 (tp-100) REVERT: U 358 MET cc_start: 0.5204 (ppp) cc_final: 0.4069 (pmm) REVERT: V 90 VAL cc_start: -0.2166 (OUTLIER) cc_final: -0.2668 (t) REVERT: W 48 MET cc_start: 0.3711 (mtt) cc_final: 0.3123 (mmt) REVERT: W 76 MET cc_start: 0.2081 (mmp) cc_final: 0.0974 (mmm) outliers start: 88 outliers final: 59 residues processed: 642 average time/residue: 1.7747 time to fit residues: 1376.4978 Evaluate side-chains 638 residues out of total 4684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 569 time to evaluate : 4.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 287 ASN Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 696 SER Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 853 LYS Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain A residue 1052 ARG Chi-restraints excluded: chain A residue 1071 GLU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1147 SER Chi-restraints excluded: chain A residue 1288 ILE Chi-restraints excluded: chain A residue 1339 ASP Chi-restraints excluded: chain A residue 1341 VAL Chi-restraints excluded: chain A residue 1437 ASP Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 214 LYS Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 312 GLN Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 503 ASN Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 556 ILE Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 710 ILE Chi-restraints excluded: chain B residue 731 GLN Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 828 VAL Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain C residue 17 GLU Chi-restraints excluded: chain C residue 26 THR Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain E residue 41 LYS Chi-restraints excluded: chain G residue 5 ILE Chi-restraints excluded: chain H residue 14 ASP Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 103 GLU Chi-restraints excluded: chain H residue 147 LYS Chi-restraints excluded: chain I residue 41 ASN Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain L residue 53 VAL Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 282 ASP Chi-restraints excluded: chain O residue 328 ILE Chi-restraints excluded: chain Q residue 156 THR Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 211 VAL Chi-restraints excluded: chain V residue 90 VAL Chi-restraints excluded: chain W residue 66 LEU Chi-restraints excluded: chain W residue 115 GLU Chi-restraints excluded: chain W residue 146 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 526 random chunks: chunk 331 optimal weight: 30.0000 chunk 444 optimal weight: 0.9980 chunk 127 optimal weight: 0.7980 chunk 384 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 115 optimal weight: 4.9990 chunk 417 optimal weight: 20.0000 chunk 174 optimal weight: 0.2980 chunk 429 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 ASN A 295 GLN A 296 ASN A 861 GLN ** A1194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1236 ASN B 585 ASN H 76 ASN I 22 ASN K 89 ASN M 263 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.206053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.120046 restraints weight = 46559.142| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.62 r_work: 0.3033 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 45231 Z= 0.241 Angle : 0.563 14.564 61434 Z= 0.284 Chirality : 0.042 0.211 6849 Planarity : 0.004 0.076 7660 Dihedral : 12.447 59.614 6734 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.77 % Allowed : 16.89 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.12), residues: 5233 helix: 1.21 (0.12), residues: 1970 sheet: 0.40 (0.18), residues: 816 loop : -0.13 (0.13), residues: 2447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 479 HIS 0.012 0.001 HIS M 18 PHE 0.024 0.002 PHE A 112 TYR 0.020 0.001 TYR E 90 ARG 0.015 0.000 ARG A 241 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22752.06 seconds wall clock time: 403 minutes 33.02 seconds (24213.02 seconds total)