Starting phenix.real_space_refine on Fri May 10 21:11:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpf_37715/05_2024/8wpf_37715_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpf_37715/05_2024/8wpf_37715.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpf_37715/05_2024/8wpf_37715_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpf_37715/05_2024/8wpf_37715_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpf_37715/05_2024/8wpf_37715_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpf_37715/05_2024/8wpf_37715.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpf_37715/05_2024/8wpf_37715.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpf_37715/05_2024/8wpf_37715_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpf_37715/05_2024/8wpf_37715_updated.pdb" } resolution = 3.0 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= 0.003 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 75 5.49 5 Mg 1 5.21 5 S 77 5.16 5 C 10544 2.51 5 N 2839 2.21 5 O 3360 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 10": "OE1" <-> "OE2" Residue "A PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 28": "OE1" <-> "OE2" Residue "A TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 210": "OE1" <-> "OE2" Residue "A TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 529": "OE1" <-> "OE2" Residue "A GLU 602": "OE1" <-> "OE2" Residue "A GLU 706": "OE1" <-> "OE2" Residue "A TYR 806": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 36": "OE1" <-> "OE2" Residue "B PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 140": "OD1" <-> "OD2" Residue "B TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 365": "OE1" <-> "OE2" Residue "B GLU 380": "OE1" <-> "OE2" Residue "B TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 192": "OD1" <-> "OD2" Residue "E GLU 168": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 16896 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: 3547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3547 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 10, 'TRANS': 425} 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: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 830 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 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: 9.05, per 1000 atoms: 0.54 Number of scatterers: 16896 At special positions: 0 Unit cell: (129.48, 131.97, 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 75 15.00 Mg 1 11.99 O 3360 8.00 N 2839 7.00 C 10544 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: 6.91 Conformation dependent library (CDL) restraints added in 2.7 seconds 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3654 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 59 helices and 25 sheets defined 40.5% alpha, 17.1% beta 31 base pairs and 56 stacking pairs defined. Time for finding SS restraints: 8.36 Creating SS restraints... Processing helix chain 'A' and resid 44 through 49 Processing helix chain 'A' and resid 109 through 116 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 218 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: 3.682A 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: 3.794A pdb=" N LYS A 503 " --> pdb=" O SER A 499 " (cutoff:3.500A) removed outlier: 3.749A 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 643 Processing helix chain 'A' and resid 647 through 672 removed outlier: 3.926A pdb=" N MET A 671 " --> pdb=" O VAL A 667 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY A 672 " --> pdb=" O TYR A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 702 Processing helix chain 'A' and resid 764 through 780 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 889 No H-bonds generated for 'chain 'A' and resid 887 through 889' 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 20 through 22 No H-bonds generated for 'chain 'B' and resid 20 through 22' Processing helix chain 'B' and resid 25 through 41 Processing helix chain 'B' and resid 108 through 120 Processing helix chain 'B' and resid 148 through 157 removed outlier: 3.575A pdb=" N LYS B 153 " --> pdb=" O VAL B 149 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU B 154 " --> pdb=" O ASN B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 187 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 322 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 360 Processing helix chain 'B' and resid 365 through 374 removed outlier: 3.764A pdb=" N ASN B 374 " --> pdb=" O THR B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 396 No H-bonds generated for 'chain 'B' and resid 394 through 396' Processing helix chain 'B' and resid 398 through 405 Processing helix chain 'B' and resid 407 through 424 Processing helix chain 'C' and resid 20 through 37 removed outlier: 5.012A pdb=" N SER C 24 " --> pdb=" O PRO C 21 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN C 25 " --> pdb=" O VAL C 22 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N VAL C 27 " --> pdb=" O SER C 24 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASN C 31 " --> pdb=" O GLU C 28 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ALA C 34 " --> pdb=" O ASN C 31 " (cutoff:3.500A) removed outlier: 4.545A 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: 5.441A pdb=" N LYS C 139 " --> pdb=" O ILE C 135 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ILE C 140 " --> pdb=" O TYR C 136 " (cutoff:3.500A) removed outlier: 3.810A 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 191 removed outlier: 3.816A pdb=" N GLN C 188 " --> pdb=" O ARG C 185 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N PHE C 189 " --> pdb=" O ASP C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 204 removed outlier: 3.515A pdb=" N ASN C 199 " --> pdb=" O PHE C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 215 Processing helix chain 'D' and resid 142 through 173 removed outlier: 3.676A pdb=" N ASP D 169 " --> pdb=" O THR D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 200 removed outlier: 4.301A pdb=" N LYS D 199 " --> pdb=" O GLU D 195 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N VAL D 200 " --> pdb=" O GLY D 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 163 Processing helix chain 'E' and resid 169 through 194 Processing helix chain 'F' and resid 143 through 173 removed outlier: 3.547A pdb=" N ASP F 152 " --> pdb=" O ASN F 148 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEU F 153 " --> pdb=" O ILE F 149 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS F 154 " --> pdb=" O VAL F 150 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LYS F 155 " --> pdb=" O LYS F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 199 Processing helix chain 'G' and resid 142 through 163 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: 4.633A pdb=" N LYS A 151 " --> pdb=" O SER A 126 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N CYS A 124 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LYS A 21 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N TRP A 8 " --> pdb=" O TYR A 19 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N TYR A 19 " --> pdb=" O TRP A 8 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N GLU A 10 " --> pdb=" O PHE A 17 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N PHE A 17 " --> pdb=" O GLU A 10 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN A 136 " --> pdb=" O CYS A 139 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N HIS A 141 " --> pdb=" O LYS A 134 " (cutoff:3.500A) removed outlier: 5.405A 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: 3.585A pdb=" N VAL A 42 " --> pdb=" O TRP A 89 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY A 61 " --> pdb=" O MET A 88 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU A 90 " --> pdb=" O PRO A 59 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N GLU A 92 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 5.619A 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: 3.699A pdb=" N ASP A 166 " --> pdb=" O SER A 187 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N SER A 184 " --> pdb=" O ASN A 204 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N LEU A 222 " --> pdb=" O LEU A 238 " (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 356 through 358 Processing sheet with id= G, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.151A pdb=" N THR A 369 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ARG A 363 " --> pdb=" O GLU A 367 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N GLU A 367 " --> pdb=" O ARG A 363 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG A 407 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N SER A 420 " --> pdb=" O VAL A 405 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N VAL A 405 " --> pdb=" O SER A 420 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 394 through 397 Processing sheet with id= I, first strand: chain 'A' and resid 822 through 826 removed outlier: 6.977A pdb=" N ILE A 547 " --> pdb=" O GLU A 792 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N VAL A 794 " --> pdb=" O VAL A 545 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N VAL A 545 " --> pdb=" O VAL A 794 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR A 749 " --> pdb=" O PHE A 756 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N GLU A 758 " --> pdb=" O SER A 747 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N SER A 747 " --> pdb=" O GLU A 758 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 596 through 601 removed outlier: 3.635A pdb=" N GLU A 611 " --> pdb=" O CYS A 601 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY A 570 " --> pdb=" O ILE A 614 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ASP A 616 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LEU A 568 " --> pdb=" O ASP A 616 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 706 through 708 Processing sheet with id= L, first strand: chain 'A' and resid 892 through 895 removed outlier: 3.952A pdb=" N TYR A 929 " --> pdb=" O ILE A 954 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 933 through 935 Processing sheet with id= N, first strand: chain 'A' and resid 299 through 305 Processing sheet with id= O, first strand: chain 'A' and resid 799 through 802 removed outlier: 7.185A pdb=" N LYS A 805 " --> pdb=" O GLN A 801 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 69 through 71 removed outlier: 3.679A pdb=" N PHE B 69 " --> pdb=" O PHE B 176 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE B 71 " --> pdb=" O THR B 174 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N THR B 174 " --> pdb=" O ILE B 71 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 166 through 170 removed outlier: 4.266A pdb=" N LEU B 166 " --> pdb=" O PHE B 78 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY B 74 " --> pdb=" O ILE B 170 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN B 208 " --> pdb=" O TYR B 199 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 95 through 97 Processing sheet with id= S, first strand: chain 'B' and resid 214 through 219 removed outlier: 3.691A pdb=" N LYS B 214 " --> pdb=" O LYS B 268 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET B 218 " --> pdb=" O VAL B 264 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL B 264 " --> pdb=" O MET B 218 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 244 through 246 Processing sheet with id= U, first strand: chain 'B' and resid 301 through 304 Processing sheet with id= V, first strand: chain 'B' and resid 124 through 128 removed outlier: 7.525A pdb=" N ILE B 142 " --> pdb=" O ASP B 125 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N LEU B 127 " --> pdb=" O ASP B 140 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ASP B 140 " --> pdb=" O LEU B 127 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'B' and resid 375 through 380 removed outlier: 6.688A pdb=" N GLU B 380 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N VAL B 384 " --> pdb=" O GLU B 380 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 2 through 5 removed outlier: 3.502A pdb=" N ILE C 13 " --> pdb=" O VAL C 4 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 116 through 120 removed outlier: 6.844A pdb=" N VAL C 62 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N TRP C 119 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N VAL C 64 " --> pdb=" O TRP C 119 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL C 154 " --> pdb=" O CYS C 63 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N CYS C 65 " --> pdb=" O VAL C 154 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N TYR C 156 " --> pdb=" O CYS C 65 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR C 175 " --> pdb=" O LEU C 155 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N CYS C 157 " --> pdb=" O THR C 175 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE C 177 " --> pdb=" O CYS C 157 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y 691 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 56 stacking parallelities Total time for adding SS restraints: 7.70 Time building geometry restraints manager: 7.52 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: 2628 1.30 - 1.43: 4843 1.43 - 1.56: 9629 1.56 - 1.69: 153 1.69 - 1.81: 120 Bond restraints: 17373 Sorted by residual: bond pdb=" C4' AAB I 6 " pdb=" O4' AAB I 6 " ideal model delta sigma weight residual 1.293 1.636 -0.343 2.00e-02 2.50e+03 2.95e+02 bond pdb=" O4' AAB I 6 " pdb=" C1' AAB I 6 " ideal model delta sigma weight residual 1.601 1.278 0.323 2.00e-02 2.50e+03 2.60e+02 bond pdb=" C4' AAB I 6 " pdb=" C3' AAB I 6 " ideal model delta sigma weight residual 1.576 1.300 0.276 2.00e-02 2.50e+03 1.91e+02 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=" C2' AAB I 6 " pdb=" C1' AAB I 6 " ideal model delta sigma weight residual 1.341 1.568 -0.227 2.00e-02 2.50e+03 1.28e+02 ... (remaining 17368 not shown) Histogram of bond angle deviations from ideal: 74.00 - 88.32: 2 88.32 - 102.63: 149 102.63 - 116.95: 12355 116.95 - 131.27: 11229 131.27 - 145.58: 52 Bond angle restraints: 23787 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 93.79 26.41 1.50e+00 4.44e-01 3.10e+02 angle pdb=" O3' DG H 34 " pdb=" P DC H 35 " pdb=" OP2 DC H 35 " ideal model delta sigma weight residual 108.00 145.58 -37.58 3.00e+00 1.11e-01 1.57e+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 74.00 34.00 3.00e+00 1.11e-01 1.28e+02 angle pdb=" CB LYS A 196 " pdb=" CG LYS A 196 " pdb=" CD LYS A 196 " ideal model delta sigma weight residual 111.30 87.49 23.81 2.30e+00 1.89e-01 1.07e+02 angle pdb=" CB MET A 492 " pdb=" CG MET A 492 " pdb=" SD MET A 492 " ideal model delta sigma weight residual 112.70 140.22 -27.52 3.00e+00 1.11e-01 8.42e+01 ... (remaining 23782 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.14: 9748 31.14 - 62.27: 583 62.27 - 93.41: 16 93.41 - 124.55: 0 124.55 - 155.68: 1 Dihedral angle restraints: 10348 sinusoidal: 4700 harmonic: 5648 Sorted by residual: dihedral pdb=" CA LEU A 165 " pdb=" C LEU A 165 " pdb=" N ASP A 166 " pdb=" CA ASP A 166 " ideal model delta harmonic sigma weight residual 180.00 149.55 30.45 0 5.00e+00 4.00e-02 3.71e+01 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 -151.66 -28.34 0 5.00e+00 4.00e-02 3.21e+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 180.00 152.44 27.56 0 5.00e+00 4.00e-02 3.04e+01 ... (remaining 10345 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.134: 2602 0.134 - 0.268: 83 0.268 - 0.401: 9 0.401 - 0.535: 1 0.535 - 0.669: 2 Chirality restraints: 2697 Sorted by residual: chirality pdb=" CG LEU A 76 " pdb=" CB LEU A 76 " pdb=" CD1 LEU A 76 " pdb=" CD2 LEU A 76 " both_signs ideal model delta sigma weight residual False -2.59 -1.92 -0.67 2.00e-01 2.50e+01 1.12e+01 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 -2.93 -0.59 2.00e-01 2.50e+01 8.65e+00 chirality pdb=" CB ILE B 137 " pdb=" CA ILE B 137 " pdb=" CG1 ILE B 137 " pdb=" CG2 ILE B 137 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.47 2.00e-01 2.50e+01 5.47e+00 ... (remaining 2694 not shown) Planarity restraints: 2755 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 172 " -0.109 5.00e-02 4.00e+02 1.60e-01 4.07e+01 pdb=" N PRO C 173 " 0.276 5.00e-02 4.00e+02 pdb=" CA PRO C 173 " -0.087 5.00e-02 4.00e+02 pdb=" CD PRO C 173 " -0.080 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 602 " 0.016 2.00e-02 2.50e+03 3.29e-02 1.08e+01 pdb=" CD GLU A 602 " -0.057 2.00e-02 2.50e+03 pdb=" OE1 GLU A 602 " 0.020 2.00e-02 2.50e+03 pdb=" OE2 GLU A 602 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 159 " 0.280 9.50e-02 1.11e+02 1.25e-01 9.79e+00 pdb=" NE ARG D 159 " -0.019 2.00e-02 2.50e+03 pdb=" CZ ARG D 159 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG D 159 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG D 159 " 0.008 2.00e-02 2.50e+03 ... (remaining 2752 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 173 2.60 - 3.17: 13529 3.17 - 3.75: 29710 3.75 - 4.32: 40693 4.32 - 4.90: 64331 Nonbonded interactions: 148436 Sorted by model distance: nonbonded pdb=" O1G D3T A2001 " pdb="MG MG A2002 " model vdw 2.020 2.170 nonbonded pdb=" OD2 ASP A 753 " pdb="MG MG A2002 " model vdw 2.026 2.170 nonbonded pdb=" O2B D3T A2001 " pdb="MG MG A2002 " model vdw 2.051 2.170 nonbonded pdb=" O TYR A 550 " pdb="MG MG A2002 " model vdw 2.170 2.170 nonbonded pdb=" OG SER B 85 " pdb=" OD2 ASP B 249 " model vdw 2.249 2.440 ... (remaining 148431 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: 1.400 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: 5.920 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 52.190 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.080 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:12.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 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 : 0.009 0.343 17373 Z= 0.514 Angle : 1.143 37.584 23787 Z= 0.582 Chirality : 0.062 0.669 2697 Planarity : 0.008 0.160 2755 Dihedral : 17.292 155.682 6694 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % 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 : 0.05 % 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: -1.58 (0.17), residues: 1894 helix: -1.25 (0.15), residues: 808 sheet: -0.20 (0.30), residues: 313 loop : -0.97 (0.20), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 8 HIS 0.027 0.002 HIS A 141 PHE 0.040 0.003 PHE A 108 TYR 0.034 0.003 TYR C 122 ARG 0.031 0.001 ARG B 135 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 251 time to evaluate : 1.767 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 ILE cc_start: 0.6304 (mt) cc_final: 0.5763 (mt) REVERT: A 89 TRP cc_start: 0.6670 (m100) cc_final: 0.6379 (m100) REVERT: A 914 TYR cc_start: 0.7722 (t80) cc_final: 0.6966 (t80) REVERT: B -10 MET cc_start: 0.3551 (tpt) cc_final: 0.1095 (mmm) REVERT: G 182 MET cc_start: 0.3740 (mmm) cc_final: 0.3466 (mmm) outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 1.0450 time to fit residues: 300.6168 Evaluate side-chains 178 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 1.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 162 optimal weight: 0.6980 chunk 146 optimal weight: 0.6980 chunk 81 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 91 optimal weight: 0.0370 chunk 112 optimal weight: 2.9990 chunk 175 optimal weight: 10.0000 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 HIS ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 785 ASN A 801 GLN A 899 ASN ** B 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 339 ASN ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 HIS ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 17373 Z= 0.206 Angle : 0.574 11.691 23787 Z= 0.307 Chirality : 0.041 0.205 2697 Planarity : 0.005 0.087 2755 Dihedral : 17.947 156.498 2893 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.60 % Allowed : 9.54 % Favored : 88.86 % 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: -0.58 (0.18), residues: 1894 helix: 0.03 (0.17), residues: 808 sheet: -0.41 (0.28), residues: 343 loop : -0.63 (0.21), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 470 HIS 0.003 0.001 HIS C 16 PHE 0.016 0.001 PHE B 126 TYR 0.017 0.001 TYR A 188 ARG 0.006 0.000 ARG A 577 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 213 time to evaluate : 2.250 Fit side-chains revert: symmetry clash REVERT: A 711 MET cc_start: 0.6432 (tpp) cc_final: 0.6209 (mmt) REVERT: B -10 MET cc_start: 0.3191 (tpt) cc_final: 0.2209 (mtp) REVERT: B 161 ASN cc_start: 0.5294 (OUTLIER) cc_final: 0.5049 (m-40) outliers start: 28 outliers final: 11 residues processed: 230 average time/residue: 1.0291 time to fit residues: 272.9280 Evaluate side-chains 182 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 170 time to evaluate : 1.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 842 MET Chi-restraints excluded: chain A residue 955 ASP Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 161 ASN Chi-restraints excluded: chain B residue 237 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 97 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 175 optimal weight: 10.0000 chunk 189 optimal weight: 2.9990 chunk 156 optimal weight: 1.9990 chunk 174 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 140 optimal weight: 0.9980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN A 250 GLN ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 ASN A 716 ASN ** A 839 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 899 ASN B -6 HIS ** B 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 ASN ** C 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 GLN F 171 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 17373 Z= 0.404 Angle : 0.682 10.693 23787 Z= 0.361 Chirality : 0.046 0.212 2697 Planarity : 0.005 0.067 2755 Dihedral : 18.461 161.335 2893 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.97 % Allowed : 13.31 % Favored : 83.71 % 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 (0.19), residues: 1894 helix: 0.19 (0.18), residues: 815 sheet: -0.89 (0.27), residues: 362 loop : -0.56 (0.22), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 19 HIS 0.012 0.002 HIS C 16 PHE 0.019 0.002 PHE A 200 TYR 0.026 0.002 TYR A 637 ARG 0.007 0.001 ARG C 193 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 209 time to evaluate : 1.913 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8169 (OUTLIER) cc_final: 0.7615 (p90) REVERT: A 642 LYS cc_start: 0.7332 (mptt) cc_final: 0.7050 (ttpp) REVERT: A 820 VAL cc_start: 0.8607 (p) cc_final: 0.8295 (p) REVERT: B 95 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.7706 (tpt) REVERT: B 266 VAL cc_start: 0.7596 (p) cc_final: 0.7300 (p) outliers start: 52 outliers final: 16 residues processed: 240 average time/residue: 1.1171 time to fit residues: 306.5616 Evaluate side-chains 186 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 168 time to evaluate : 1.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 955 ASP Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain E residue 157 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 173 optimal weight: 5.9990 chunk 132 optimal weight: 7.9990 chunk 91 optimal weight: 0.5980 chunk 19 optimal weight: 0.3980 chunk 83 optimal weight: 0.9990 chunk 117 optimal weight: 9.9990 chunk 176 optimal weight: 7.9990 chunk 186 optimal weight: 10.0000 chunk 92 optimal weight: 0.9990 chunk 167 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 716 ASN A 801 GLN ** A 917 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B -6 HIS ** B 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 17373 Z= 0.230 Angle : 0.564 9.417 23787 Z= 0.300 Chirality : 0.041 0.233 2697 Planarity : 0.004 0.057 2755 Dihedral : 18.203 161.075 2893 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.03 % Allowed : 15.54 % Favored : 81.43 % 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: -0.26 (0.19), residues: 1894 helix: 0.56 (0.18), residues: 812 sheet: -0.88 (0.27), residues: 333 loop : -0.47 (0.22), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 470 HIS 0.005 0.001 HIS A 839 PHE 0.015 0.002 PHE B 410 TYR 0.017 0.002 TYR A 637 ARG 0.005 0.000 ARG C 193 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 190 time to evaluate : 1.942 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8090 (OUTLIER) cc_final: 0.7549 (p90) REVERT: A 209 THR cc_start: 0.7209 (p) cc_final: 0.6879 (m) REVERT: A 521 GLU cc_start: 0.6218 (OUTLIER) cc_final: 0.5780 (pt0) REVERT: A 642 LYS cc_start: 0.7329 (mptt) cc_final: 0.7039 (ttpp) REVERT: A 734 LYS cc_start: 0.7604 (tptp) cc_final: 0.7254 (tptt) REVERT: A 820 VAL cc_start: 0.8608 (OUTLIER) cc_final: 0.8263 (p) REVERT: B 343 THR cc_start: 0.7054 (t) cc_final: 0.6735 (m) REVERT: C 2 ASN cc_start: 0.6496 (OUTLIER) cc_final: 0.5986 (m-40) REVERT: F 182 MET cc_start: 0.6182 (OUTLIER) cc_final: 0.5435 (mpp) REVERT: G 182 MET cc_start: 0.4431 (mmm) cc_final: 0.4137 (mmm) outliers start: 53 outliers final: 25 residues processed: 223 average time/residue: 1.1544 time to fit residues: 293.3183 Evaluate side-chains 202 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 172 time to evaluate : 1.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 362 ASN Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 521 GLU Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain A residue 888 GLU Chi-restraints excluded: chain A residue 955 ASP Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain B residue 43 TRP Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain C residue 2 ASN Chi-restraints excluded: chain C residue 25 GLN Chi-restraints excluded: chain E residue 161 SER Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain F residue 182 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 155 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 138 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 159 optimal weight: 0.6980 chunk 128 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 167 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 HIS A 136 ASN ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 716 ASN A 917 ASN B -6 HIS ** B 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 HIS ** C 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 17373 Z= 0.310 Angle : 0.592 9.129 23787 Z= 0.314 Chirality : 0.042 0.178 2697 Planarity : 0.004 0.055 2755 Dihedral : 18.250 162.210 2893 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 17.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.71 % Allowed : 15.89 % Favored : 80.40 % 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: -0.21 (0.19), residues: 1894 helix: 0.63 (0.18), residues: 812 sheet: -0.88 (0.27), residues: 351 loop : -0.45 (0.22), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 470 HIS 0.004 0.001 HIS B -9 PHE 0.023 0.002 PHE A 992 TYR 0.020 0.002 TYR A 637 ARG 0.006 0.000 ARG C 58 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 189 time to evaluate : 1.848 Fit side-chains revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8191 (OUTLIER) cc_final: 0.7701 (p90) REVERT: A 341 LEU cc_start: 0.8130 (mt) cc_final: 0.7894 (mp) REVERT: A 521 GLU cc_start: 0.6528 (OUTLIER) cc_final: 0.6091 (pt0) REVERT: A 642 LYS cc_start: 0.7350 (mptt) cc_final: 0.7075 (ttpp) REVERT: A 820 VAL cc_start: 0.8616 (OUTLIER) cc_final: 0.8246 (p) REVERT: B 266 VAL cc_start: 0.7706 (OUTLIER) cc_final: 0.7430 (p) REVERT: B 343 THR cc_start: 0.7212 (t) cc_final: 0.6914 (m) REVERT: F 182 MET cc_start: 0.6168 (OUTLIER) cc_final: 0.5502 (mpp) REVERT: G 182 MET cc_start: 0.4522 (mmm) cc_final: 0.4193 (mmm) outliers start: 65 outliers final: 26 residues processed: 229 average time/residue: 1.1142 time to fit residues: 292.7895 Evaluate side-chains 205 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 174 time to evaluate : 1.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain A residue 362 ASN Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 521 GLU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 955 ASP Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain B residue 43 TRP Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain C residue 2 ASN Chi-restraints excluded: chain E residue 161 SER Chi-restraints excluded: chain F residue 182 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 62 optimal weight: 0.9990 chunk 168 optimal weight: 5.9990 chunk 36 optimal weight: 0.5980 chunk 109 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 186 optimal weight: 10.0000 chunk 155 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN A 170 HIS ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 716 ASN ** B -6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 17373 Z= 0.298 Angle : 0.580 7.398 23787 Z= 0.309 Chirality : 0.042 0.172 2697 Planarity : 0.004 0.054 2755 Dihedral : 18.230 162.364 2893 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 17.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.31 % Allowed : 17.31 % Favored : 79.37 % 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: 1894 helix: 0.68 (0.18), residues: 817 sheet: -0.87 (0.27), residues: 351 loop : -0.41 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 470 HIS 0.006 0.001 HIS B -9 PHE 0.021 0.002 PHE A 992 TYR 0.023 0.002 TYR A 300 ARG 0.003 0.000 ARG C 193 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 188 time to evaluate : 1.998 Fit side-chains revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8184 (OUTLIER) cc_final: 0.7722 (p90) REVERT: A 341 LEU cc_start: 0.8152 (mt) cc_final: 0.7913 (mp) REVERT: A 521 GLU cc_start: 0.6584 (OUTLIER) cc_final: 0.6128 (pt0) REVERT: A 642 LYS cc_start: 0.7343 (mptt) cc_final: 0.7071 (ttpp) REVERT: A 734 LYS cc_start: 0.7542 (tptp) cc_final: 0.7230 (tptt) REVERT: A 820 VAL cc_start: 0.8681 (OUTLIER) cc_final: 0.8324 (p) REVERT: B 266 VAL cc_start: 0.7671 (OUTLIER) cc_final: 0.7413 (p) REVERT: B 343 THR cc_start: 0.7212 (t) cc_final: 0.6884 (m) REVERT: E 170 VAL cc_start: 0.8327 (m) cc_final: 0.8087 (m) REVERT: F 182 MET cc_start: 0.6129 (OUTLIER) cc_final: 0.5496 (mpp) REVERT: G 182 MET cc_start: 0.4463 (mmm) cc_final: 0.4144 (mmm) outliers start: 58 outliers final: 30 residues processed: 230 average time/residue: 1.1258 time to fit residues: 294.9644 Evaluate side-chains 208 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 173 time to evaluate : 1.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 521 GLU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 769 GLU Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 824 ILE Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 955 ASP Chi-restraints excluded: chain B residue 43 TRP Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 230 ASP Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain C residue 2 ASN Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain E residue 161 SER Chi-restraints excluded: chain F residue 182 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 180 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 106 optimal weight: 8.9990 chunk 136 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 chunk 157 optimal weight: 2.9990 chunk 104 optimal weight: 0.6980 chunk 186 optimal weight: 10.0000 chunk 116 optimal weight: 5.9990 chunk 113 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN A 147 ASN ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 716 ASN ** B -6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 351 GLN ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.106 17373 Z= 0.379 Angle : 0.633 9.997 23787 Z= 0.334 Chirality : 0.044 0.183 2697 Planarity : 0.004 0.055 2755 Dihedral : 18.452 163.797 2893 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 18.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.71 % Allowed : 16.80 % Favored : 79.49 % 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: -0.28 (0.19), residues: 1894 helix: 0.53 (0.18), residues: 821 sheet: -0.98 (0.27), residues: 342 loop : -0.41 (0.22), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 89 HIS 0.008 0.001 HIS B -9 PHE 0.020 0.002 PHE A 992 TYR 0.028 0.002 TYR A 300 ARG 0.006 0.001 ARG C 193 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 187 time to evaluate : 1.885 Fit side-chains REVERT: A 37 TYR cc_start: 0.8309 (OUTLIER) cc_final: 0.7866 (p90) REVERT: A 642 LYS cc_start: 0.7344 (mptt) cc_final: 0.7049 (ttpp) REVERT: A 820 VAL cc_start: 0.8702 (OUTLIER) cc_final: 0.8363 (p) REVERT: B -10 MET cc_start: 0.7309 (tpt) cc_final: 0.6964 (tpt) REVERT: B 266 VAL cc_start: 0.7712 (OUTLIER) cc_final: 0.7461 (p) REVERT: B 343 THR cc_start: 0.7245 (t) cc_final: 0.6917 (m) REVERT: F 182 MET cc_start: 0.6167 (OUTLIER) cc_final: 0.5510 (mpp) outliers start: 65 outliers final: 32 residues processed: 230 average time/residue: 1.1525 time to fit residues: 301.3909 Evaluate side-chains 213 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 177 time to evaluate : 1.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 71 THR Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 656 MET Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 724 MET Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 769 GLU Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 955 ASP Chi-restraints excluded: chain A residue 977 SER Chi-restraints excluded: chain B residue 43 TRP Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain C residue 2 ASN Chi-restraints excluded: chain E residue 161 SER Chi-restraints excluded: chain F residue 182 MET Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain G residue 192 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 115 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 118 optimal weight: 9.9990 chunk 126 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 146 optimal weight: 0.9980 chunk 169 optimal weight: 9.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 716 ASN ** B -6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 351 GLN ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 17373 Z= 0.255 Angle : 0.575 8.827 23787 Z= 0.305 Chirality : 0.041 0.164 2697 Planarity : 0.004 0.055 2755 Dihedral : 18.244 163.809 2893 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 17.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.51 % Allowed : 19.37 % Favored : 78.11 % 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: -0.09 (0.19), residues: 1894 helix: 0.74 (0.18), residues: 811 sheet: -0.97 (0.28), residues: 327 loop : -0.33 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 470 HIS 0.005 0.001 HIS B -9 PHE 0.021 0.002 PHE A 992 TYR 0.027 0.002 TYR A 300 ARG 0.005 0.000 ARG C 193 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 192 time to evaluate : 1.895 Fit side-chains revert: symmetry clash REVERT: A 37 TYR cc_start: 0.8227 (OUTLIER) cc_final: 0.7823 (p90) REVERT: A 642 LYS cc_start: 0.7344 (mptt) cc_final: 0.7064 (ttpp) REVERT: A 820 VAL cc_start: 0.8651 (OUTLIER) cc_final: 0.8300 (p) REVERT: B 266 VAL cc_start: 0.7655 (OUTLIER) cc_final: 0.7412 (p) REVERT: B 343 THR cc_start: 0.7233 (t) cc_final: 0.6938 (m) REVERT: F 182 MET cc_start: 0.6122 (OUTLIER) cc_final: 0.5460 (mpp) outliers start: 44 outliers final: 23 residues processed: 218 average time/residue: 1.1323 time to fit residues: 281.7692 Evaluate side-chains 207 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 180 time to evaluate : 2.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 724 MET Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 769 GLU Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 955 ASP Chi-restraints excluded: chain B residue 43 TRP Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain C residue 2 ASN Chi-restraints excluded: chain F residue 182 MET Chi-restraints excluded: chain G residue 166 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 178 optimal weight: 7.9990 chunk 162 optimal weight: 0.6980 chunk 173 optimal weight: 0.5980 chunk 104 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 136 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 156 optimal weight: 1.9990 chunk 163 optimal weight: 0.7980 chunk 172 optimal weight: 0.7980 chunk 113 optimal weight: 9.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B -6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 351 GLN ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 17373 Z= 0.238 Angle : 0.571 9.516 23787 Z= 0.302 Chirality : 0.041 0.170 2697 Planarity : 0.004 0.055 2755 Dihedral : 18.142 163.793 2893 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.17 % Allowed : 19.94 % Favored : 77.89 % 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: -0.03 (0.19), residues: 1894 helix: 0.78 (0.18), residues: 818 sheet: -0.97 (0.27), residues: 334 loop : -0.29 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 470 HIS 0.004 0.001 HIS B -9 PHE 0.023 0.002 PHE A 55 TYR 0.031 0.002 TYR A 300 ARG 0.007 0.000 ARG C 193 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 196 time to evaluate : 1.692 Fit side-chains REVERT: A 37 TYR cc_start: 0.8196 (OUTLIER) cc_final: 0.7805 (p90) REVERT: A 642 LYS cc_start: 0.7287 (mptt) cc_final: 0.7051 (ttpp) REVERT: A 820 VAL cc_start: 0.8642 (OUTLIER) cc_final: 0.8272 (p) REVERT: A 920 GLU cc_start: 0.6710 (mm-30) cc_final: 0.6503 (mm-30) REVERT: B 343 THR cc_start: 0.7248 (t) cc_final: 0.6960 (m) REVERT: F 182 MET cc_start: 0.6142 (OUTLIER) cc_final: 0.5456 (mpp) outliers start: 38 outliers final: 26 residues processed: 221 average time/residue: 1.0503 time to fit residues: 266.1068 Evaluate side-chains 212 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 183 time to evaluate : 2.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 724 MET Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 769 GLU Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 955 ASP Chi-restraints excluded: chain B residue 43 TRP Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain C residue 2 ASN Chi-restraints excluded: chain F residue 182 MET Chi-restraints excluded: chain G residue 166 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 183 optimal weight: 0.0370 chunk 111 optimal weight: 0.6980 chunk 86 optimal weight: 0.9990 chunk 127 optimal weight: 3.9990 chunk 192 optimal weight: 10.0000 chunk 176 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 118 optimal weight: 9.9990 chunk 93 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 overall best weight: 0.9262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B -6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 351 GLN ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 17373 Z= 0.261 Angle : 0.583 10.219 23787 Z= 0.307 Chirality : 0.041 0.168 2697 Planarity : 0.004 0.054 2755 Dihedral : 18.150 163.766 2893 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 17.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.57 % Allowed : 20.00 % Favored : 77.43 % 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: -0.04 (0.19), residues: 1894 helix: 0.77 (0.18), residues: 818 sheet: -0.99 (0.27), residues: 330 loop : -0.28 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 470 HIS 0.004 0.001 HIS B -9 PHE 0.022 0.002 PHE A 55 TYR 0.035 0.002 TYR A 300 ARG 0.007 0.000 ARG C 193 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 183 time to evaluate : 1.713 Fit side-chains REVERT: A 37 TYR cc_start: 0.8216 (OUTLIER) cc_final: 0.7740 (p90) REVERT: A 642 LYS cc_start: 0.7280 (mptt) cc_final: 0.7035 (ttpp) REVERT: A 820 VAL cc_start: 0.8652 (OUTLIER) cc_final: 0.8280 (p) REVERT: B 343 THR cc_start: 0.7236 (t) cc_final: 0.6969 (m) REVERT: F 182 MET cc_start: 0.6151 (OUTLIER) cc_final: 0.5459 (mpp) outliers start: 45 outliers final: 28 residues processed: 212 average time/residue: 1.1115 time to fit residues: 272.0164 Evaluate side-chains 209 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 178 time to evaluate : 1.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 TYR Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 359 LYS Chi-restraints excluded: chain A residue 476 GLU Chi-restraints excluded: chain A residue 695 ILE Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 724 MET Chi-restraints excluded: chain A residue 753 ASP Chi-restraints excluded: chain A residue 757 THR Chi-restraints excluded: chain A residue 769 GLU Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 820 VAL Chi-restraints excluded: chain A residue 831 THR Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 955 ASP Chi-restraints excluded: chain B residue 43 TRP Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 249 ASP Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 391 ASN Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain C residue 2 ASN Chi-restraints excluded: chain F residue 182 MET Chi-restraints excluded: chain G residue 166 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 163 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 141 optimal weight: 0.9990 chunk 22 optimal weight: 0.0870 chunk 42 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 157 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 overall best weight: 0.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN ** A 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B -6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.181698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.151159 restraints weight = 18610.587| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 1.27 r_work: 0.3425 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 17373 Z= 0.238 Angle : 0.576 9.425 23787 Z= 0.302 Chirality : 0.041 0.169 2697 Planarity : 0.004 0.054 2755 Dihedral : 18.084 163.713 2893 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.11 % Allowed : 20.57 % Favored : 77.31 % 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: -0.01 (0.19), residues: 1894 helix: 0.81 (0.18), residues: 819 sheet: -0.92 (0.28), residues: 327 loop : -0.32 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 470 HIS 0.005 0.001 HIS B -9 PHE 0.022 0.002 PHE A 55 TYR 0.029 0.002 TYR A 300 ARG 0.007 0.000 ARG C 193 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5214.30 seconds wall clock time: 95 minutes 20.58 seconds (5720.58 seconds total)