Starting phenix.real_space_refine on Sun Mar 17 05:41:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpk_37717/03_2024/8wpk_37717_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpk_37717/03_2024/8wpk_37717.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpk_37717/03_2024/8wpk_37717_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpk_37717/03_2024/8wpk_37717_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpk_37717/03_2024/8wpk_37717_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpk_37717/03_2024/8wpk_37717.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpk_37717/03_2024/8wpk_37717.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpk_37717/03_2024/8wpk_37717_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpk_37717/03_2024/8wpk_37717_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 72 5.49 5 Mg 1 5.21 5 S 77 5.16 5 C 10525 2.51 5 N 2832 2.21 5 O 3347 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 45": "OE1" <-> "OE2" Residue "A ASP 77": "OD1" <-> "OD2" Residue "A PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 122": "OD1" <-> "OD2" Residue "A TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 192": "OD1" <-> "OD2" Residue "A GLU 235": "OE1" <-> "OE2" Residue "A TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 339": "OE1" <-> "OE2" Residue "A TYR 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 495": "OE1" <-> "OE2" Residue "A GLU 699": "OE1" <-> "OE2" Residue "A ASP 753": "OD1" <-> "OD2" Residue "A GLU 758": "OE1" <-> "OE2" Residue "A GLU 790": "OE1" <-> "OE2" Residue "A GLU 792": "OE1" <-> "OE2" Residue "A GLU 873": "OE1" <-> "OE2" Residue "A TYR 914": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 967": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 969": "OE1" <-> "OE2" Residue "A PHE 993": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 139": "OE1" <-> "OE2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 279": "OD1" <-> "OD2" Residue "B TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 337": "OE1" <-> "OE2" Residue "B PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 18": "OD1" <-> "OD2" Residue "C GLU 32": "OE1" <-> "OE2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "C TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 196": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16854 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 8223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 8223 Classifications: {'peptide': 1006} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 37, 'TRANS': 968} Chain: "B" Number of atoms: 3557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3557 Classifications: {'peptide': 437} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 426} Chain: "C" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1773 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 204} Chain: "D" Number of atoms: 525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 525 Classifications: {'peptide': 69} Link IDs: {'TRANS': 68} Chain: "E" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 425 Classifications: {'peptide': 57} Link IDs: {'TRANS': 56} Chain: "F" Number of atoms: 481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 481 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 64} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 425 Classifications: {'peptide': 57} Link IDs: {'TRANS': 56} Chain: "H" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 638 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 778 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'D3T': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.92, per 1000 atoms: 0.53 Number of scatterers: 16854 At special positions: 0 Unit cell: (129.48, 132.8, 136.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 77 16.00 P 72 15.00 Mg 1 11.99 O 3347 8.00 N 2832 7.00 C 10525 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: 6.90 Conformation dependent library (CDL) restraints added in 2.7 seconds 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3656 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 58 helices and 23 sheets defined 40.5% alpha, 15.8% beta 31 base pairs and 57 stacking pairs defined. Time for finding SS restraints: 8.33 Creating SS restraints... Processing helix chain 'A' and resid 44 through 48 Processing helix chain 'A' and resid 109 through 116 Processing helix chain 'A' and resid 129 through 131 No H-bonds generated for 'chain 'A' and resid 129 through 131' Processing helix chain 'A' and resid 145 through 148 No H-bonds generated for 'chain 'A' and resid 145 through 148' Processing helix chain 'A' and resid 210 through 219 Processing helix chain 'A' and resid 241 through 252 Processing helix chain 'A' and resid 268 through 279 Processing helix chain 'A' and resid 331 through 338 Processing helix chain 'A' and resid 346 through 353 Processing helix chain 'A' and resid 381 through 389 Processing helix chain 'A' and resid 440 through 445 Processing helix chain 'A' and resid 449 through 473 removed outlier: 3.597A pdb=" N GLN A 467 " --> pdb=" O ALA A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 486 Processing helix chain 'A' and resid 490 through 492 No H-bonds generated for 'chain 'A' and resid 490 through 492' Processing helix chain 'A' and resid 498 through 512 removed outlier: 3.837A pdb=" N GLY A 504 " --> pdb=" O THR A 500 " (cutoff:3.500A) Proline residue: A 505 - end of helix Processing helix chain 'A' and resid 553 through 560 Processing helix chain 'A' and resid 577 through 590 Processing helix chain 'A' and resid 622 through 642 Processing helix chain 'A' and resid 647 through 671 removed outlier: 3.973A pdb=" N MET A 671 " --> pdb=" O VAL A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 702 Processing helix chain 'A' and resid 764 through 781 Processing helix chain 'A' and resid 837 through 856 Processing helix chain 'A' and resid 861 through 882 Processing helix chain 'A' and resid 887 through 890 Processing helix chain 'A' and resid 906 through 917 Processing helix chain 'A' and resid 948 through 950 No H-bonds generated for 'chain 'A' and resid 948 through 950' Processing helix chain 'A' and resid 968 through 982 Processing helix chain 'A' and resid 986 through 997 Processing helix chain 'B' and resid 4 through 18 Processing helix chain 'B' and resid 25 through 41 Processing helix chain 'B' and resid 108 through 120 Processing helix chain 'B' and resid 149 through 157 removed outlier: 4.146A pdb=" N LYS B 153 " --> pdb=" O VAL B 149 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU B 154 " --> pdb=" O ASN B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 188 Processing helix chain 'B' and resid 250 through 255 Processing helix chain 'B' and resid 286 through 297 Processing helix chain 'B' and resid 316 through 323 Processing helix chain 'B' and resid 331 through 340 Processing helix chain 'B' and resid 342 through 350 Processing helix chain 'B' and resid 353 through 361 Processing helix chain 'B' and resid 365 through 374 removed outlier: 3.573A pdb=" N ASN B 374 " --> pdb=" O THR B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 396 removed outlier: 3.541A pdb=" N ASN B 396 " --> pdb=" O ASN B 393 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 393 through 396' Processing helix chain 'B' and resid 398 through 425 removed outlier: 4.908A pdb=" N ASN B 408 " --> pdb=" O TYR B 404 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N GLN B 409 " --> pdb=" O GLY B 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 37 Proline residue: C 21 - end of helix removed outlier: 5.733A pdb=" N SER C 24 " --> pdb=" O PRO C 21 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLN C 25 " --> pdb=" O VAL C 22 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE C 29 " --> pdb=" O LEU C 26 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR C 30 " --> pdb=" O VAL C 27 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ALA C 34 " --> pdb=" O ASN C 31 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N SER C 35 " --> pdb=" O GLU C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 48 No H-bonds generated for 'chain 'C' and resid 46 through 48' Processing helix chain 'C' and resid 87 through 100 Processing helix chain 'C' and resid 134 through 151 removed outlier: 5.803A pdb=" N LYS C 139 " --> pdb=" O ILE C 135 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N ILE C 140 " --> pdb=" O TYR C 136 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N HIS C 151 " --> pdb=" O HIS C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 169 No H-bonds generated for 'chain 'C' and resid 166 through 169' Processing helix chain 'C' and resid 185 through 187 No H-bonds generated for 'chain 'C' and resid 185 through 187' Processing helix chain 'C' and resid 194 through 204 Processing helix chain 'C' and resid 212 through 215 Processing helix chain 'D' and resid 143 through 172 removed outlier: 3.731A pdb=" N ASP D 169 " --> pdb=" O THR D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 197 Processing helix chain 'E' and resid 141 through 163 Processing helix chain 'E' and resid 169 through 195 Processing helix chain 'F' and resid 143 through 172 removed outlier: 3.684A pdb=" N ASP F 152 " --> pdb=" O ASN F 148 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS F 155 " --> pdb=" O LYS F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 200 Processing helix chain 'G' and resid 142 through 165 removed outlier: 4.956A pdb=" N THR G 165 " --> pdb=" O SER G 161 " (cutoff:3.500A) Processing helix chain 'G' and resid 169 through 194 Processing sheet with id= A, first strand: chain 'A' and resid 151 through 153 removed outlier: 4.474A pdb=" N LYS A 151 " --> pdb=" O SER A 126 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N CYS A 124 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LYS A 21 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N TRP A 8 " --> pdb=" O TYR A 19 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N TYR A 19 " --> pdb=" O TRP A 8 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLU A 10 " --> pdb=" O PHE A 17 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N PHE A 17 " --> pdb=" O GLU A 10 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN A 136 " --> pdb=" O CYS A 139 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N HIS A 141 " --> pdb=" O LYS A 134 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N LYS A 134 " --> pdb=" O HIS A 141 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 38 through 43 removed outlier: 3.902A pdb=" N GLY A 61 " --> pdb=" O MET A 88 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LEU A 90 " --> pdb=" O PRO A 59 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N GLU A 92 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N ALA A 57 " --> pdb=" O GLU A 92 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 64 through 67 Processing sheet with id= D, first strand: chain 'A' and resid 327 through 330 removed outlier: 6.877A pdb=" N SER A 184 " --> pdb=" O ASN A 204 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 285 through 287 Processing sheet with id= F, first strand: chain 'A' and resid 428 through 432 removed outlier: 7.073A pdb=" N THR A 369 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ARG A 363 " --> pdb=" O GLU A 367 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLU A 367 " --> pdb=" O ARG A 363 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 394 through 397 Processing sheet with id= H, first strand: chain 'A' and resid 822 through 826 removed outlier: 6.946A pdb=" N ILE A 547 " --> pdb=" O GLU A 792 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N VAL A 794 " --> pdb=" O VAL A 545 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N VAL A 545 " --> pdb=" O VAL A 794 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR A 749 " --> pdb=" O PHE A 756 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N GLU A 758 " --> pdb=" O SER A 747 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N SER A 747 " --> pdb=" O GLU A 758 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 596 through 601 removed outlier: 3.670A pdb=" N GLU A 611 " --> pdb=" O CYS A 601 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY A 570 " --> pdb=" O ILE A 614 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ASP A 616 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N LEU A 568 " --> pdb=" O ASP A 616 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 706 through 708 Processing sheet with id= K, first strand: chain 'A' and resid 892 through 895 removed outlier: 3.886A pdb=" N TYR A 929 " --> pdb=" O ILE A 954 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 933 through 935 Processing sheet with id= M, first strand: chain 'A' and resid 299 through 305 Processing sheet with id= N, first strand: chain 'A' and resid 799 through 802 removed outlier: 7.049A pdb=" N LYS A 805 " --> pdb=" O GLN A 801 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 95 through 97 Processing sheet with id= P, first strand: chain 'B' and resid 208 through 210 removed outlier: 3.665A pdb=" N GLN B 208 " --> pdb=" O TYR B 199 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL B 81 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ILE B 197 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU B 79 " --> pdb=" O ILE B 197 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N TYR B 199 " --> pdb=" O ILE B 77 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ILE B 77 " --> pdb=" O TYR B 199 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 214 through 216 removed outlier: 3.568A pdb=" N LYS B 214 " --> pdb=" O LYS B 268 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 244 through 246 removed outlier: 3.530A pdb=" N VAL B 237 " --> pdb=" O ILE B 245 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 302 through 304 Processing sheet with id= T, first strand: chain 'B' and resid 124 through 128 removed outlier: 7.452A pdb=" N ILE B 142 " --> pdb=" O ASP B 125 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N LEU B 127 " --> pdb=" O ASP B 140 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ASP B 140 " --> pdb=" O LEU B 127 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 375 through 379 removed outlier: 3.729A pdb=" N ASN B 386 " --> pdb=" O LYS B 378 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 2 through 4 Processing sheet with id= W, first strand: chain 'C' and resid 116 through 120 removed outlier: 6.687A pdb=" N VAL C 62 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N TRP C 119 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N VAL C 64 " --> pdb=" O TRP C 119 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL C 154 " --> pdb=" O CYS C 63 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N CYS C 65 " --> pdb=" O VAL C 154 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N TYR C 156 " --> pdb=" O CYS C 65 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N THR C 175 " --> pdb=" O LEU C 155 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N CYS C 157 " --> pdb=" O THR C 175 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ILE C 177 " --> pdb=" O CYS C 157 " (cutoff:3.500A) No H-bonds generated for sheet with id= W 689 hydrogen bonds defined for protein. 1974 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 78 hydrogen bonds 156 hydrogen bond angles 0 basepair planarities 31 basepair parallelities 57 stacking parallelities Total time for adding SS restraints: 7.60 Time building geometry restraints manager: 7.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 2623 1.30 - 1.43: 4805 1.43 - 1.56: 9629 1.56 - 1.68: 148 1.68 - 1.81: 120 Bond restraints: 17325 Sorted by residual: bond pdb=" C4' D3T A2001 " pdb=" C3' D3T A2001 " ideal model delta sigma weight residual 1.287 1.515 -0.228 2.00e-02 2.50e+03 1.30e+02 bond pdb=" C4' DC H 35 " pdb=" C3' DC H 35 " ideal model delta sigma weight residual 1.523 1.327 0.196 2.00e-02 2.50e+03 9.61e+01 bond pdb=" C4' D3T A2001 " pdb=" O4' D3T A2001 " ideal model delta sigma weight residual 1.614 1.426 0.188 2.00e-02 2.50e+03 8.86e+01 bond pdb=" C2 D3T A2001 " pdb=" N3 D3T A2001 " ideal model delta sigma weight residual 1.493 1.331 0.162 2.00e-02 2.50e+03 6.54e+01 bond pdb=" C4' DC H 35 " pdb=" O4' DC H 35 " ideal model delta sigma weight residual 1.450 1.609 -0.159 2.00e-02 2.50e+03 6.28e+01 ... (remaining 17320 not shown) Histogram of bond angle deviations from ideal: 84.20 - 94.17: 1 94.17 - 104.14: 393 104.14 - 114.11: 10278 114.11 - 124.08: 12474 124.08 - 134.05: 567 Bond angle restraints: 23713 Sorted by residual: angle pdb=" C3' DG H 34 " pdb=" O3' DG H 34 " pdb=" P DC H 35 " ideal model delta sigma weight residual 120.20 100.32 19.88 1.50e+00 4.44e-01 1.76e+02 angle pdb=" O3' DG H 34 " pdb=" P DC H 35 " pdb=" O5' DC H 35 " ideal model delta sigma weight residual 104.00 120.43 -16.43 1.50e+00 4.44e-01 1.20e+02 angle pdb=" O3' DG H 34 " pdb=" P DC H 35 " pdb=" OP1 DC H 35 " ideal model delta sigma weight residual 108.00 84.20 23.80 3.00e+00 1.11e-01 6.30e+01 angle pdb=" CA MET E 182 " pdb=" CB MET E 182 " pdb=" CG MET E 182 " ideal model delta sigma weight residual 114.10 124.25 -10.15 2.00e+00 2.50e-01 2.57e+01 angle pdb=" N ALA C 9 " pdb=" CA ALA C 9 " pdb=" C ALA C 9 " ideal model delta sigma weight residual 109.81 120.19 -10.38 2.21e+00 2.05e-01 2.21e+01 ... (remaining 23708 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.32: 9732 31.32 - 62.63: 567 62.63 - 93.95: 20 93.95 - 125.26: 1 125.26 - 156.58: 1 Dihedral angle restraints: 10321 sinusoidal: 4670 harmonic: 5651 Sorted by residual: dihedral pdb=" CA GLU G 168 " pdb=" C GLU G 168 " pdb=" N ASP G 169 " pdb=" CA ASP G 169 " ideal model delta harmonic sigma weight residual -180.00 -151.22 -28.78 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA SER C 43 " pdb=" C SER C 43 " pdb=" N PRO C 44 " pdb=" CA PRO C 44 " ideal model delta harmonic sigma weight residual 180.00 151.75 28.25 0 5.00e+00 4.00e-02 3.19e+01 dihedral pdb=" CA VAL A 667 " pdb=" C VAL A 667 " pdb=" N TYR A 668 " pdb=" CA TYR A 668 " ideal model delta harmonic sigma weight residual 180.00 157.32 22.68 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 10318 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 2600 0.119 - 0.238: 79 0.238 - 0.357: 4 0.357 - 0.477: 1 0.477 - 0.596: 3 Chirality restraints: 2687 Sorted by residual: chirality pdb=" P DC H 35 " pdb=" OP1 DC H 35 " pdb=" OP2 DC H 35 " pdb=" O5' DC H 35 " both_signs ideal model delta sigma weight residual True 2.35 -2.94 -0.60 2.00e-01 2.50e+01 8.87e+00 chirality pdb=" CB ILE B 274 " pdb=" CA ILE B 274 " pdb=" CG1 ILE B 274 " pdb=" CG2 ILE B 274 " both_signs ideal model delta sigma weight residual False 2.64 2.06 0.58 2.00e-01 2.50e+01 8.41e+00 chirality pdb=" CB ILE C 135 " pdb=" CA ILE C 135 " pdb=" CG1 ILE C 135 " pdb=" CG2 ILE C 135 " both_signs ideal model delta sigma weight residual False 2.64 2.16 0.48 2.00e-01 2.50e+01 5.81e+00 ... (remaining 2684 not shown) Planarity restraints: 2756 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 162 " 0.047 5.00e-02 4.00e+02 7.13e-02 8.14e+00 pdb=" N PRO B 163 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO B 163 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 163 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 668 " -0.032 2.00e-02 2.50e+03 1.96e-02 7.70e+00 pdb=" CG TYR A 668 " -0.001 2.00e-02 2.50e+03 pdb=" CD1 TYR A 668 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR A 668 " 0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR A 668 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 668 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 668 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 668 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 713 " -0.200 9.50e-02 1.11e+02 9.04e-02 6.44e+00 pdb=" NE ARG A 713 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG A 713 " -0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG A 713 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG A 713 " -0.000 2.00e-02 2.50e+03 ... (remaining 2753 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 237 2.65 - 3.21: 14440 3.21 - 3.77: 29868 3.77 - 4.34: 40646 4.34 - 4.90: 62686 Nonbonded interactions: 147877 Sorted by model distance: nonbonded pdb=" OD2 ASP A 753 " pdb="MG MG A2002 " model vdw 2.082 2.170 nonbonded pdb=" O3A D3T A2001 " pdb="MG MG A2002 " model vdw 2.096 2.170 nonbonded pdb=" OD2 ASP A 549 " pdb="MG MG A2002 " model vdw 2.127 2.170 nonbonded pdb=" O TYR A 550 " pdb="MG MG A2002 " model vdw 2.168 2.170 nonbonded pdb=" O VAL A 475 " pdb=" OG1 THR A 479 " model vdw 2.220 2.440 ... (remaining 147872 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'D' and (resid 139 through 201 or (resid 202 through 203 and (name N or n \ ame CA or name C or name O or name CB )))) selection = chain 'F' } ncs_group { reference = chain 'E' selection = chain 'G' } 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: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.450 Check model and map are aligned: 0.260 Set scattering table: 0.150 Process input model: 52.680 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.090 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:11.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 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 : 0.007 0.228 17325 Z= 0.393 Angle : 0.876 23.803 23713 Z= 0.474 Chirality : 0.055 0.596 2687 Planarity : 0.007 0.090 2756 Dihedral : 17.188 156.575 6665 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.80 % Favored : 97.15 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.17), residues: 1895 helix: -0.89 (0.15), residues: 828 sheet: -1.00 (0.27), residues: 371 loop : -0.83 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 36 HIS 0.007 0.001 HIS A 839 PHE 0.024 0.003 PHE A 108 TYR 0.032 0.002 TYR A 668 ARG 0.021 0.001 ARG A 713 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 243 time to evaluate : 1.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 440 LEU cc_start: 0.8289 (mt) cc_final: 0.8050 (mt) REVERT: A 524 GLN cc_start: 0.6928 (tp-100) cc_final: 0.6695 (mm-40) REVERT: C 17 ASP cc_start: 0.6976 (m-30) cc_final: 0.6586 (m-30) REVERT: C 36 TRP cc_start: 0.8065 (m100) cc_final: 0.7643 (m100) REVERT: C 68 ASP cc_start: 0.7211 (p0) cc_final: 0.6974 (p0) REVERT: F 182 MET cc_start: 0.1331 (mmm) cc_final: -0.0075 (tmm) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 1.1077 time to fit residues: 304.3779 Evaluate side-chains 184 residues out of total 1753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 2.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 98 optimal weight: 8.9990 chunk 77 optimal weight: 3.9990 chunk 150 optimal weight: 0.5980 chunk 58 optimal weight: 0.5980 chunk 91 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 174 optimal weight: 9.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN A 600 HIS A 703 ASN A 801 GLN ** B -8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B -6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 ASN B 146 GLN B 161 ASN C 109 ASN C 146 GLN ** C 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17325 Z= 0.208 Angle : 0.528 7.973 23713 Z= 0.291 Chirality : 0.040 0.142 2687 Planarity : 0.004 0.059 2756 Dihedral : 17.757 158.214 2861 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.11 % Favored : 97.84 % Rotamer: Outliers : 2.00 % Allowed : 6.91 % Favored : 91.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.19), residues: 1895 helix: 0.40 (0.17), residues: 831 sheet: -0.78 (0.27), residues: 365 loop : -0.44 (0.23), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 940 HIS 0.005 0.001 HIS A 839 PHE 0.019 0.001 PHE A 992 TYR 0.021 0.001 TYR A 637 ARG 0.008 0.000 ARG A 713 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 208 time to evaluate : 1.924 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 263 ASN cc_start: 0.8304 (t0) cc_final: 0.8089 (t0) REVERT: A 347 ASP cc_start: 0.7644 (OUTLIER) cc_final: 0.7044 (p0) REVERT: A 440 LEU cc_start: 0.8386 (mt) cc_final: 0.8185 (mt) REVERT: A 512 GLU cc_start: 0.6879 (OUTLIER) cc_final: 0.6676 (tt0) REVERT: A 602 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.6627 (pp20) REVERT: C 17 ASP cc_start: 0.7408 (m-30) cc_final: 0.6908 (m-30) REVERT: F 182 MET cc_start: 0.1324 (mmm) cc_final: -0.0093 (tmm) outliers start: 35 outliers final: 13 residues processed: 224 average time/residue: 1.2017 time to fit residues: 303.0423 Evaluate side-chains 192 residues out of total 1753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 176 time to evaluate : 1.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 921 THR Chi-restraints excluded: chain A residue 978 GLU Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 135 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 3.9990 chunk 54 optimal weight: 0.4980 chunk 145 optimal weight: 0.8980 chunk 118 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 chunk 174 optimal weight: 0.9980 chunk 188 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 chunk 173 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 140 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN A 703 ASN A 801 GLN ** B -8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B -6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 ASN B 146 GLN B 318 GLN C 146 GLN ** C 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 211 ASN C 214 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17325 Z= 0.208 Angle : 0.518 8.088 23713 Z= 0.283 Chirality : 0.040 0.216 2687 Planarity : 0.004 0.049 2756 Dihedral : 17.797 160.021 2861 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.27 % Favored : 97.68 % Rotamer: Outliers : 2.11 % Allowed : 10.22 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.19), residues: 1895 helix: 0.92 (0.18), residues: 833 sheet: -0.72 (0.27), residues: 362 loop : -0.33 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 470 HIS 0.004 0.001 HIS A 839 PHE 0.026 0.001 PHE A 992 TYR 0.018 0.001 TYR A 637 ARG 0.006 0.000 ARG A 713 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 189 time to evaluate : 2.019 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 196 LYS cc_start: 0.8379 (ttpt) cc_final: 0.8162 (ttpt) REVERT: A 263 ASN cc_start: 0.8348 (t0) cc_final: 0.8097 (t0) REVERT: A 347 ASP cc_start: 0.7669 (OUTLIER) cc_final: 0.7121 (p0) REVERT: A 512 GLU cc_start: 0.6939 (OUTLIER) cc_final: 0.6718 (tt0) REVERT: A 602 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.6204 (pp20) REVERT: B 22 PHE cc_start: 0.5646 (m-80) cc_final: 0.5010 (m-80) REVERT: F 182 MET cc_start: 0.1313 (mmm) cc_final: -0.0105 (tmm) outliers start: 37 outliers final: 14 residues processed: 208 average time/residue: 1.1783 time to fit residues: 277.0217 Evaluate side-chains 187 residues out of total 1753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 170 time to evaluate : 1.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 921 THR Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 978 GLU Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 135 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 172 optimal weight: 5.9990 chunk 131 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 117 optimal weight: 8.9990 chunk 175 optimal weight: 30.0000 chunk 185 optimal weight: 20.0000 chunk 91 optimal weight: 0.9990 chunk 166 optimal weight: 20.0000 chunk 50 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN A 225 GLN A 307 HIS A 450 ASN A 801 GLN ** B -8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B -6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 ASN ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 252 HIS B 397 ASN C 146 GLN ** C 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 17325 Z= 0.433 Angle : 0.644 12.458 23713 Z= 0.347 Chirality : 0.045 0.225 2687 Planarity : 0.005 0.055 2756 Dihedral : 18.200 165.326 2861 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.43 % Favored : 97.52 % Rotamer: Outliers : 2.40 % Allowed : 12.34 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.19), residues: 1895 helix: 0.94 (0.18), residues: 824 sheet: -0.77 (0.28), residues: 354 loop : -0.25 (0.23), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 940 HIS 0.008 0.001 HIS A 839 PHE 0.028 0.002 PHE A 992 TYR 0.026 0.002 TYR A 637 ARG 0.008 0.001 ARG A 713 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 183 time to evaluate : 3.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 223 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.7637 (ttt-90) REVERT: A 235 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.6690 (mp0) REVERT: A 602 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.6230 (pp20) REVERT: B 199 TYR cc_start: 0.6316 (p90) cc_final: 0.6020 (p90) REVERT: E 182 MET cc_start: 0.5522 (tpt) cc_final: 0.5310 (mmt) REVERT: F 182 MET cc_start: 0.1497 (mmm) cc_final: -0.0010 (tmm) outliers start: 42 outliers final: 20 residues processed: 208 average time/residue: 1.2327 time to fit residues: 287.7988 Evaluate side-chains 184 residues out of total 1753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 161 time to evaluate : 1.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ARG Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 921 THR Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 978 GLU Chi-restraints excluded: chain B residue 22 PHE Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 184 MET Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain C residue 32 GLU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain E residue 171 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 154 optimal weight: 0.2980 chunk 105 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 138 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 158 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 0 optimal weight: 0.5980 chunk 94 optimal weight: 0.9980 chunk 166 optimal weight: 8.9990 chunk 46 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN A 703 ASN A 981 ASN ** B -8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B -6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 ASN B 146 GLN B 397 ASN ** C 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 ASN G 148 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17325 Z= 0.196 Angle : 0.525 8.655 23713 Z= 0.286 Chirality : 0.040 0.141 2687 Planarity : 0.004 0.044 2756 Dihedral : 17.988 164.434 2861 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.37 % Favored : 97.57 % Rotamer: Outliers : 2.40 % Allowed : 13.65 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.20), residues: 1895 helix: 1.19 (0.18), residues: 825 sheet: -0.81 (0.27), residues: 369 loop : -0.03 (0.24), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 470 HIS 0.005 0.001 HIS B -9 PHE 0.022 0.001 PHE A 992 TYR 0.019 0.001 TYR A 637 ARG 0.008 0.000 ARG A 713 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 180 time to evaluate : 1.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.6688 (mp0) REVERT: A 492 MET cc_start: 0.7520 (mmm) cc_final: 0.7318 (mmp) REVERT: B 176 PHE cc_start: 0.5452 (OUTLIER) cc_final: 0.4183 (m-80) REVERT: B 199 TYR cc_start: 0.5944 (p90) cc_final: 0.5719 (p90) REVERT: C 191 LYS cc_start: 0.7866 (OUTLIER) cc_final: 0.7522 (mtmt) REVERT: F 182 MET cc_start: 0.1344 (mmm) cc_final: -0.0088 (tmm) outliers start: 42 outliers final: 15 residues processed: 207 average time/residue: 1.2732 time to fit residues: 293.7927 Evaluate side-chains 181 residues out of total 1753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 163 time to evaluate : 1.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 921 THR Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain B residue 22 PHE Chi-restraints excluded: chain B residue 52 ASN Chi-restraints excluded: chain B residue 176 PHE Chi-restraints excluded: chain B residue 184 MET Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain C residue 192 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 62 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 45 optimal weight: 0.6980 chunk 185 optimal weight: 9.9990 chunk 154 optimal weight: 0.2980 chunk 86 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN A 981 ASN ** B -8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B -6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 ASN ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 ASN ** C 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 17325 Z= 0.293 Angle : 0.566 9.767 23713 Z= 0.307 Chirality : 0.042 0.144 2687 Planarity : 0.004 0.046 2756 Dihedral : 18.064 170.435 2861 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.57 % Allowed : 14.68 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.20), residues: 1895 helix: 1.19 (0.18), residues: 822 sheet: -0.85 (0.26), residues: 377 loop : -0.09 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 940 HIS 0.007 0.001 HIS B -9 PHE 0.021 0.002 PHE A 992 TYR 0.021 0.002 TYR A 637 ARG 0.008 0.000 ARG A 713 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 164 time to evaluate : 1.840 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 235 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.6695 (mp0) REVERT: A 978 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.7074 (tt0) REVERT: B 318 GLN cc_start: 0.6946 (mm-40) cc_final: 0.6613 (mm-40) REVERT: C 191 LYS cc_start: 0.7871 (OUTLIER) cc_final: 0.7506 (mtmt) REVERT: F 182 MET cc_start: 0.1373 (mmm) cc_final: -0.0084 (tmm) outliers start: 45 outliers final: 23 residues processed: 196 average time/residue: 1.2099 time to fit residues: 267.5960 Evaluate side-chains 181 residues out of total 1753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 155 time to evaluate : 1.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain A residue 373 ASP Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 921 THR Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 978 GLU Chi-restraints excluded: chain B residue 22 PHE Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 52 ASN Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain C residue 192 ASP Chi-restraints excluded: chain E residue 171 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 179 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 185 optimal weight: 10.0000 chunk 115 optimal weight: 9.9990 chunk 112 optimal weight: 10.0000 chunk 85 optimal weight: 9.9990 chunk 114 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN A 981 ASN ** B -8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B -6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 ASN B 146 GLN ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 GLN ** C 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 ASN G 178 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 17325 Z= 0.402 Angle : 0.638 11.821 23713 Z= 0.344 Chirality : 0.045 0.223 2687 Planarity : 0.005 0.055 2756 Dihedral : 18.203 172.153 2861 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.08 % Allowed : 14.56 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.20), residues: 1895 helix: 1.03 (0.18), residues: 822 sheet: -0.89 (0.27), residues: 358 loop : -0.15 (0.24), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 940 HIS 0.010 0.001 HIS B -9 PHE 0.022 0.002 PHE A 630 TYR 0.024 0.002 TYR A 637 ARG 0.007 0.001 ARG A 713 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 177 time to evaluate : 1.840 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 LYS cc_start: 0.7629 (OUTLIER) cc_final: 0.7238 (tptp) REVERT: A 235 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.6730 (mp0) REVERT: A 406 ILE cc_start: 0.8420 (mm) cc_final: 0.8094 (mt) REVERT: A 978 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.7045 (tt0) REVERT: C 191 LYS cc_start: 0.7932 (OUTLIER) cc_final: 0.7526 (mtmt) REVERT: F 182 MET cc_start: 0.1523 (mmm) cc_final: 0.0004 (tmm) REVERT: G 178 GLN cc_start: 0.3582 (OUTLIER) cc_final: 0.3067 (tt0) REVERT: G 182 MET cc_start: 0.2735 (OUTLIER) cc_final: 0.1865 (mmt) outliers start: 54 outliers final: 25 residues processed: 213 average time/residue: 1.1758 time to fit residues: 282.2371 Evaluate side-chains 199 residues out of total 1753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 168 time to evaluate : 1.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 LYS Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 921 THR Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 978 GLU Chi-restraints excluded: chain B residue 22 PHE Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 52 ASN Chi-restraints excluded: chain B residue 66 ASN Chi-restraints excluded: chain B residue 137 ILE Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain C residue 2 ASN Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain C residue 192 ASP Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain G residue 178 GLN Chi-restraints excluded: chain G residue 182 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 117 optimal weight: 0.0980 chunk 126 optimal weight: 4.9990 chunk 91 optimal weight: 0.2980 chunk 17 optimal weight: 0.1980 chunk 145 optimal weight: 0.8980 chunk 168 optimal weight: 0.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 225 GLN A 450 ASN A 981 ASN ** B -8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B -6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 ASN ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 161 ASN B 164 ASN B 386 ASN ** C 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17325 Z= 0.179 Angle : 0.523 8.057 23713 Z= 0.283 Chirality : 0.040 0.247 2687 Planarity : 0.004 0.044 2756 Dihedral : 17.971 166.030 2861 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.88 % Allowed : 16.45 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.20), residues: 1895 helix: 1.26 (0.18), residues: 825 sheet: -0.86 (0.27), residues: 372 loop : 0.03 (0.24), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 470 HIS 0.006 0.001 HIS B -9 PHE 0.022 0.001 PHE A 992 TYR 0.016 0.001 TYR A 637 ARG 0.008 0.000 ARG A 693 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 178 time to evaluate : 1.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.6691 (mp0) REVERT: C 191 LYS cc_start: 0.7862 (OUTLIER) cc_final: 0.7481 (mtmt) REVERT: F 182 MET cc_start: 0.1580 (mmm) cc_final: 0.0026 (tmm) REVERT: G 182 MET cc_start: 0.2470 (OUTLIER) cc_final: 0.2167 (tpt) outliers start: 33 outliers final: 18 residues processed: 198 average time/residue: 1.3101 time to fit residues: 292.4185 Evaluate side-chains 187 residues out of total 1753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 166 time to evaluate : 1.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 921 THR Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain C residue 2 ASN Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain C residue 192 ASP Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain G residue 182 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 177 optimal weight: 5.9990 chunk 161 optimal weight: 2.9990 chunk 172 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 135 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 chunk 171 optimal weight: 3.9990 chunk 113 optimal weight: 10.0000 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 450 ASN A 703 ASN A 981 ASN ** B -8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B -6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 ASN ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 ASN ** C 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 17325 Z= 0.341 Angle : 0.601 10.403 23713 Z= 0.323 Chirality : 0.043 0.339 2687 Planarity : 0.004 0.051 2756 Dihedral : 18.159 173.605 2861 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.06 % Allowed : 16.85 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.20), residues: 1895 helix: 1.16 (0.18), residues: 822 sheet: -0.82 (0.27), residues: 355 loop : -0.07 (0.24), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 940 HIS 0.009 0.001 HIS B -9 PHE 0.027 0.002 PHE A 55 TYR 0.022 0.002 TYR A 637 ARG 0.008 0.000 ARG A 693 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 173 time to evaluate : 1.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 GLU cc_start: 0.6566 (pm20) cc_final: 0.6359 (pm20) REVERT: A 978 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.7076 (tt0) REVERT: B 184 MET cc_start: 0.5039 (tpp) cc_final: 0.4707 (ttp) REVERT: C 191 LYS cc_start: 0.7886 (OUTLIER) cc_final: 0.7477 (mtmt) REVERT: F 182 MET cc_start: 0.1581 (mmm) cc_final: 0.0036 (tmm) REVERT: G 182 MET cc_start: 0.2428 (OUTLIER) cc_final: 0.2195 (tpt) outliers start: 36 outliers final: 22 residues processed: 197 average time/residue: 1.1880 time to fit residues: 264.5768 Evaluate side-chains 197 residues out of total 1753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 172 time to evaluate : 1.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 921 THR Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 978 GLU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain C residue 2 ASN Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain C residue 192 ASP Chi-restraints excluded: chain E residue 171 GLN Chi-restraints excluded: chain G residue 182 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 182 optimal weight: 20.0000 chunk 111 optimal weight: 0.5980 chunk 86 optimal weight: 5.9990 chunk 126 optimal weight: 0.9990 chunk 191 optimal weight: 10.0000 chunk 176 optimal weight: 4.9990 chunk 152 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 117 optimal weight: 0.0670 chunk 93 optimal weight: 1.9990 chunk 120 optimal weight: 0.7980 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 225 GLN A 426 ASN A 450 ASN A 703 ASN A 981 ASN ** B -8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B -6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 ASN ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 ASN B 386 ASN ** C 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17325 Z= 0.198 Angle : 0.536 8.695 23713 Z= 0.289 Chirality : 0.040 0.153 2687 Planarity : 0.004 0.045 2756 Dihedral : 17.995 165.955 2861 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.66 % Allowed : 17.42 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.20), residues: 1895 helix: 1.26 (0.18), residues: 825 sheet: -0.84 (0.27), residues: 372 loop : 0.06 (0.25), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 470 HIS 0.008 0.001 HIS B -9 PHE 0.022 0.001 PHE A 992 TYR 0.017 0.001 TYR A 637 ARG 0.010 0.000 ARG A 713 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 171 time to evaluate : 1.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.6698 (mp0) REVERT: A 978 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.7040 (tt0) REVERT: C 191 LYS cc_start: 0.7877 (OUTLIER) cc_final: 0.7478 (mtmt) REVERT: F 182 MET cc_start: 0.1591 (mmm) cc_final: 0.0040 (tmm) outliers start: 29 outliers final: 20 residues processed: 188 average time/residue: 1.2351 time to fit residues: 260.4681 Evaluate side-chains 188 residues out of total 1753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 165 time to evaluate : 1.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 867 ASP Chi-restraints excluded: chain A residue 920 GLU Chi-restraints excluded: chain A residue 921 THR Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain A residue 978 GLU Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain C residue 2 ASN Chi-restraints excluded: chain C residue 135 ILE Chi-restraints excluded: chain C residue 191 LYS Chi-restraints excluded: chain C residue 192 ASP Chi-restraints excluded: chain E residue 171 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 140 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 152 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 156 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 450 ASN A 981 ASN ** B -8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B -6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 ASN ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 386 ASN ** C 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.190937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.162529 restraints weight = 16688.208| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 1.27 r_work: 0.3584 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3531 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 17325 Z= 0.287 Angle : 0.585 9.296 23713 Z= 0.314 Chirality : 0.042 0.235 2687 Planarity : 0.004 0.049 2756 Dihedral : 18.098 169.094 2861 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.00 % Allowed : 17.02 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.20), residues: 1895 helix: 1.21 (0.18), residues: 822 sheet: -0.81 (0.27), residues: 360 loop : 0.02 (0.24), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 37 HIS 0.010 0.001 HIS B -9 PHE 0.023 0.002 PHE A 992 TYR 0.020 0.002 TYR A 637 ARG 0.011 0.000 ARG A 713 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5319.11 seconds wall clock time: 95 minutes 28.44 seconds (5728.44 seconds total)