Starting phenix.real_space_refine on Mon Dec 11 05:43:51 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpk_37717/12_2023/8wpk_37717_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpk_37717/12_2023/8wpk_37717.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpk_37717/12_2023/8wpk_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_37717/12_2023/8wpk_37717_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpk_37717/12_2023/8wpk_37717_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpk_37717/12_2023/8wpk_37717.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpk_37717/12_2023/8wpk_37717.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpk_37717/12_2023/8wpk_37717_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpk_37717/12_2023/8wpk_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-1.21rc1-5172/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: 9.32, per 1000 atoms: 0.55 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: 7.14 Conformation dependent library (CDL) restraints added in 2.6 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: 8.12 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: 7.17 Time building geometry restraints manager: 7.62 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: 1.360 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: 6.480 Check model and map are aligned: 0.260 Set scattering table: 0.170 Process input model: 53.360 Find NCS groups from input model: 0.570 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: 0.000 Load rotamer database and sin/cos tables:13.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.010 ------------------------------------------------------------------------------- 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 : 1.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 1.1585 time to fit residues: 318.6480 Evaluate side-chains 182 residues out of total 1753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 2.018 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8260 ------------------------------------------------------------------------------- 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: 4.9990 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** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17325 Z= 0.214 Angle : 0.534 8.115 23713 Z= 0.293 Chirality : 0.041 0.141 2687 Planarity : 0.004 0.058 2756 Dihedral : 17.754 158.313 2861 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.11 % Favored : 97.84 % Rotamer: Outliers : 2.06 % Allowed : 6.85 % 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: -0.36 (0.19), residues: 1895 helix: 0.38 (0.17), residues: 836 sheet: -0.77 (0.27), residues: 364 loop : -0.48 (0.23), residues: 695 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 0.006 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 245 residues out of total 1753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 209 time to evaluate : 1.934 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 12 residues processed: 225 average time/residue: 1.2170 time to fit residues: 308.9217 Evaluate side-chains 187 residues out of total 1753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 175 time to evaluate : 1.904 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 9 residues processed: 3 average time/residue: 0.2144 time to fit residues: 3.8127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 145 optimal weight: 0.2980 chunk 118 optimal weight: 5.9990 chunk 48 optimal weight: 0.6980 chunk 174 optimal weight: 7.9990 chunk 188 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 173 optimal weight: 5.9990 chunk 59 optimal weight: 0.7980 chunk 140 optimal weight: 4.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN 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 252 HIS 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 17325 Z= 0.322 Angle : 0.594 10.524 23713 Z= 0.321 Chirality : 0.043 0.195 2687 Planarity : 0.005 0.049 2756 Dihedral : 18.097 162.952 2861 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.32 % Favored : 97.63 % Rotamer: Outliers : 2.11 % Allowed : 11.02 % Favored : 86.86 % 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: 0.05 (0.19), residues: 1895 helix: 0.83 (0.18), residues: 825 sheet: -0.78 (0.27), residues: 363 loop : -0.28 (0.23), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 8 HIS 0.006 0.001 HIS A 839 PHE 0.026 0.002 PHE A 992 TYR 0.022 0.002 TYR A 637 ARG 0.007 0.001 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 233 residues out of total 1753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 196 time to evaluate : 1.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 16 residues processed: 216 average time/residue: 1.2591 time to fit residues: 305.8775 Evaluate side-chains 185 residues out of total 1753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 169 time to evaluate : 1.878 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 12 residues processed: 4 average time/residue: 0.1909 time to fit residues: 3.9067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 90 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 175 optimal weight: 20.0000 chunk 185 optimal weight: 20.0000 chunk 91 optimal weight: 2.9990 chunk 166 optimal weight: 20.0000 chunk 50 optimal weight: 0.8980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 GLN 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 397 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: 0.7765 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 17325 Z= 0.361 Angle : 0.602 11.884 23713 Z= 0.326 Chirality : 0.044 0.204 2687 Planarity : 0.005 0.052 2756 Dihedral : 18.171 178.533 2861 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.48 % Favored : 97.47 % Rotamer: Outliers : 2.63 % Allowed : 13.31 % Favored : 84.07 % 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: 0.16 (0.19), residues: 1895 helix: 0.98 (0.18), residues: 824 sheet: -0.86 (0.27), residues: 364 loop : -0.21 (0.24), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 940 HIS 0.007 0.001 HIS A 839 PHE 0.021 0.002 PHE A 992 TYR 0.024 0.002 TYR A 637 ARG 0.010 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 218 residues out of total 1753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 172 time to evaluate : 2.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 21 residues processed: 200 average time/residue: 1.2680 time to fit residues: 285.4232 Evaluate side-chains 180 residues out of total 1753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 159 time to evaluate : 1.830 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 13 residues processed: 8 average time/residue: 0.5758 time to fit residues: 8.3829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 154 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 2 optimal weight: 0.0980 chunk 138 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 158 optimal weight: 0.7980 chunk 128 optimal weight: 0.6980 chunk 0 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 chunk 166 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 164 ASN ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7707 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17325 Z= 0.219 Angle : 0.539 9.063 23713 Z= 0.292 Chirality : 0.041 0.185 2687 Planarity : 0.004 0.046 2756 Dihedral : 18.047 165.775 2861 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.48 % Favored : 97.47 % Rotamer: Outliers : 2.46 % Allowed : 14.11 % Favored : 83.44 % 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: 0.37 (0.20), residues: 1895 helix: 1.17 (0.18), residues: 826 sheet: -0.83 (0.27), residues: 375 loop : -0.07 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 470 HIS 0.006 0.001 HIS B -9 PHE 0.021 0.002 PHE A 992 TYR 0.019 0.001 TYR A 637 ARG 0.007 0.000 ARG A 693 *********************** 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 214 residues out of total 1753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 171 time to evaluate : 2.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 23 residues processed: 200 average time/residue: 1.3006 time to fit residues: 292.9876 Evaluate side-chains 182 residues out of total 1753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 159 time to evaluate : 1.896 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 15 residues processed: 8 average time/residue: 0.4483 time to fit residues: 7.3465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 62 optimal weight: 0.0980 chunk 167 optimal weight: 0.9980 chunk 36 optimal weight: 0.4980 chunk 108 optimal weight: 9.9990 chunk 45 optimal weight: 0.6980 chunk 185 optimal weight: 9.9990 chunk 154 optimal weight: 0.0020 chunk 86 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 overall best weight: 0.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 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 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 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 : 0.003 0.043 17325 Z= 0.172 Angle : 0.501 7.479 23713 Z= 0.273 Chirality : 0.039 0.135 2687 Planarity : 0.004 0.044 2756 Dihedral : 17.901 164.571 2861 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.00 % Allowed : 15.25 % 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: 0.57 (0.20), residues: 1895 helix: 1.34 (0.18), residues: 825 sheet: -0.73 (0.27), residues: 369 loop : 0.01 (0.24), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 470 HIS 0.005 0.001 HIS B -9 PHE 0.023 0.001 PHE A 992 TYR 0.017 0.001 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 220 residues out of total 1753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 185 time to evaluate : 1.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 22 residues processed: 208 average time/residue: 1.2920 time to fit residues: 302.1125 Evaluate side-chains 192 residues out of total 1753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 170 time to evaluate : 2.277 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 15 residues processed: 8 average time/residue: 0.3731 time to fit residues: 7.1038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 179 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 156 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 185 optimal weight: 9.9990 chunk 115 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 85 optimal weight: 9.9990 chunk 114 optimal weight: 4.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 161 ASN B 386 ASN B 397 ASN B 409 GLN ** 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: 0.7760 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 17325 Z= 0.340 Angle : 0.590 10.855 23713 Z= 0.318 Chirality : 0.043 0.184 2687 Planarity : 0.004 0.049 2756 Dihedral : 18.097 172.142 2861 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.28 % Allowed : 16.05 % 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: 0.41 (0.20), residues: 1895 helix: 1.18 (0.18), residues: 823 sheet: -0.75 (0.27), residues: 357 loop : -0.07 (0.24), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 940 HIS 0.008 0.001 HIS B -9 PHE 0.022 0.002 PHE A 992 TYR 0.021 0.002 TYR A 637 ARG 0.008 0.000 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 215 residues out of total 1753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 175 time to evaluate : 2.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 22 residues processed: 206 average time/residue: 1.2627 time to fit residues: 293.3981 Evaluate side-chains 189 residues out of total 1753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 167 time to evaluate : 1.984 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 16 residues processed: 6 average time/residue: 0.4297 time to fit residues: 6.2311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 0.9990 chunk 110 optimal weight: 8.9990 chunk 55 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 117 optimal weight: 9.9990 chunk 126 optimal weight: 5.9990 chunk 91 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 145 optimal weight: 0.7980 chunk 168 optimal weight: 0.0570 overall best weight: 0.6698 ------------------------------------------------------------------------------- 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 164 ASN ** B 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 17325 Z= 0.204 Angle : 0.536 7.996 23713 Z= 0.289 Chirality : 0.040 0.196 2687 Planarity : 0.004 0.049 2756 Dihedral : 17.990 164.976 2861 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.00 % Allowed : 16.56 % Favored : 81.44 % 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: 1.24 (0.18), residues: 826 sheet: -0.77 (0.27), residues: 364 loop : 0.03 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 470 HIS 0.007 0.001 HIS B -9 PHE 0.023 0.001 PHE A 992 TYR 0.018 0.001 TYR A 637 ARG 0.012 0.000 ARG A 713 *********************** 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 212 residues out of total 1753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 177 time to evaluate : 1.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 25 residues processed: 205 average time/residue: 1.3621 time to fit residues: 315.1082 Evaluate side-chains 195 residues out of total 1753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 170 time to evaluate : 3.271 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 20 residues processed: 5 average time/residue: 0.4745 time to fit residues: 7.8939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 172 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 135 optimal weight: 0.0980 chunk 52 optimal weight: 0.0870 chunk 155 optimal weight: 3.9990 chunk 163 optimal weight: 0.0670 chunk 171 optimal weight: 0.7980 chunk 113 optimal weight: 10.0000 overall best weight: 0.6098 ------------------------------------------------------------------------------- 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 164 ASN ** C 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 ASN G 178 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17325 Z= 0.194 Angle : 0.526 8.542 23713 Z= 0.284 Chirality : 0.040 0.155 2687 Planarity : 0.004 0.048 2756 Dihedral : 17.958 164.749 2861 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.83 % Allowed : 16.79 % Favored : 81.38 % 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: 0.58 (0.20), residues: 1895 helix: 1.33 (0.18), residues: 826 sheet: -0.74 (0.27), residues: 364 loop : 0.07 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 470 HIS 0.007 0.001 HIS B -9 PHE 0.023 0.001 PHE A 992 TYR 0.017 0.001 TYR A 637 ARG 0.013 0.000 ARG A 713 *********************** 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 206 residues out of total 1753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 174 time to evaluate : 1.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 25 residues processed: 200 average time/residue: 1.2980 time to fit residues: 292.1158 Evaluate side-chains 195 residues out of total 1753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 170 time to evaluate : 1.978 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 20 residues processed: 5 average time/residue: 0.2944 time to fit residues: 4.7059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 182 optimal weight: 7.9990 chunk 111 optimal weight: 0.9980 chunk 86 optimal weight: 0.0670 chunk 126 optimal weight: 5.9990 chunk 191 optimal weight: 10.0000 chunk 176 optimal weight: 5.9990 chunk 152 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 117 optimal weight: 6.9990 chunk 93 optimal weight: 0.0170 chunk 120 optimal weight: 4.9990 overall best weight: 0.7758 ------------------------------------------------------------------------------- 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 164 ASN ** C 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 17325 Z= 0.216 Angle : 0.548 10.030 23713 Z= 0.295 Chirality : 0.041 0.198 2687 Planarity : 0.004 0.048 2756 Dihedral : 17.983 164.761 2861 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.83 % Allowed : 16.96 % Favored : 81.21 % 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: 0.58 (0.20), residues: 1895 helix: 1.30 (0.18), residues: 825 sheet: -0.75 (0.27), residues: 362 loop : 0.08 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 470 HIS 0.007 0.001 HIS B -9 PHE 0.022 0.001 PHE A 992 TYR 0.017 0.001 TYR A 637 ARG 0.012 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 207 residues out of total 1753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 175 time to evaluate : 2.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 23 residues processed: 202 average time/residue: 1.2583 time to fit residues: 286.8817 Evaluate side-chains 191 residues out of total 1753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 168 time to evaluate : 1.929 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 20 residues processed: 3 average time/residue: 0.2688 time to fit residues: 3.8787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 140 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 152 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 156 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 133 optimal weight: 7.9990 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 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 164 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 = 0.4157 r_free = 0.4157 target = 0.194525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.167998 restraints weight = 16945.537| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 1.14 r_work: 0.3710 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3660 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 17325 Z= 0.224 Angle : 0.549 9.018 23713 Z= 0.296 Chirality : 0.041 0.329 2687 Planarity : 0.004 0.048 2756 Dihedral : 17.981 164.926 2861 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.71 % Allowed : 17.48 % Favored : 80.81 % 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: 0.56 (0.20), residues: 1895 helix: 1.30 (0.18), residues: 822 sheet: -0.75 (0.27), residues: 362 loop : 0.07 (0.24), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 37 HIS 0.008 0.001 HIS B -9 PHE 0.022 0.001 PHE A 992 TYR 0.018 0.001 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: 5540.34 seconds wall clock time: 101 minutes 46.59 seconds (6106.59 seconds total)