Starting phenix.real_space_refine on Mon Dec 11 05:56:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpf_37715/12_2023/8wpf_37715_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpf_37715/12_2023/8wpf_37715.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpf_37715/12_2023/8wpf_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_37715/12_2023/8wpf_37715_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpf_37715/12_2023/8wpf_37715_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpf_37715/12_2023/8wpf_37715.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpf_37715/12_2023/8wpf_37715.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpf_37715/12_2023/8wpf_37715_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpf_37715/12_2023/8wpf_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-1.21rc1-5172/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: 9.22, per 1000 atoms: 0.55 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: 7.15 Conformation dependent library (CDL) restraints added in 3.1 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: 7.97 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: 7.10 Time building geometry restraints manager: 7.72 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: 1.340 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: 0.010 Extract box with map and model: 5.880 Check model and map are aligned: 0.310 Set scattering table: 0.200 Process input model: 53.810 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.450 ------------------------------------------------------------------------------- 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 : 2.183 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.9967 time to fit residues: 287.9941 Evaluate side-chains 178 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 1.752 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5980 ------------------------------------------------------------------------------- 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: 0.9980 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: 0.7980 chunk 112 optimal weight: 2.9990 chunk 175 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 ASN ** A 589 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 785 ASN A 801 GLN ** A 899 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B -6 HIS ** 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: 0.7087 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 17373 Z= 0.226 Angle : 0.578 11.593 23787 Z= 0.310 Chirality : 0.041 0.194 2697 Planarity : 0.005 0.084 2755 Dihedral : 17.961 157.030 2893 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.77 % Allowed : 9.43 % Favored : 88.80 % 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 (0.18), residues: 1894 helix: 0.05 (0.17), residues: 808 sheet: -0.45 (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 0.004 0.001 HIS C 8 PHE 0.017 0.002 PHE A 958 TYR 0.019 0.002 TYR A 188 ARG 0.008 0.001 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 242 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 211 time to evaluate : 1.817 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 12 residues processed: 231 average time/residue: 1.0312 time to fit residues: 274.3195 Evaluate side-chains 181 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 169 time to evaluate : 1.719 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 10 residues processed: 2 average time/residue: 0.6924 time to fit residues: 4.1420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 97 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 145 optimal weight: 0.0170 chunk 119 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 175 optimal weight: 9.9990 chunk 189 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 174 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 overall best weight: 2.2026 ------------------------------------------------------------------------------- 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 716 ASN A 899 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 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 GLN F 171 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.101 17373 Z= 0.448 Angle : 0.685 10.978 23787 Z= 0.365 Chirality : 0.046 0.222 2697 Planarity : 0.005 0.069 2755 Dihedral : 18.488 161.643 2893 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.03 % Allowed : 13.03 % Favored : 83.94 % 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: -0.67 (0.18), residues: 1894 helix: 0.08 (0.18), residues: 821 sheet: -0.93 (0.26), residues: 362 loop : -0.58 (0.22), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 470 HIS 0.005 0.002 HIS A 839 PHE 0.019 0.003 PHE A 958 TYR 0.025 0.002 TYR A 637 ARG 0.008 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 256 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 203 time to evaluate : 2.045 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 21 residues processed: 236 average time/residue: 1.1026 time to fit residues: 297.4687 Evaluate side-chains 190 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 169 time to evaluate : 1.924 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 16 residues processed: 5 average time/residue: 1.0766 time to fit residues: 8.7461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 173 optimal weight: 1.9990 chunk 132 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 19 optimal weight: 0.0670 chunk 83 optimal weight: 0.8980 chunk 117 optimal weight: 7.9990 chunk 176 optimal weight: 5.9990 chunk 186 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 chunk 167 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 overall best weight: 1.1722 ------------------------------------------------------------------------------- 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 716 ASN ** 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** E 171 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 17373 Z= 0.290 Angle : 0.586 9.862 23787 Z= 0.312 Chirality : 0.042 0.231 2697 Planarity : 0.004 0.060 2755 Dihedral : 18.319 161.679 2893 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.03 % Allowed : 15.09 % Favored : 81.89 % 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: -0.41 (0.19), residues: 1894 helix: 0.43 (0.18), residues: 818 sheet: -0.91 (0.26), residues: 347 loop : -0.58 (0.22), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 470 HIS 0.005 0.001 HIS A 839 PHE 0.021 0.002 PHE A 992 TYR 0.019 0.002 TYR A 637 ARG 0.006 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 244 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 191 time to evaluate : 2.013 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 27 residues processed: 231 average time/residue: 1.0735 time to fit residues: 284.5869 Evaluate side-chains 198 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 171 time to evaluate : 2.017 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 25 residues processed: 2 average time/residue: 0.1637 time to fit residues: 3.3874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 2 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 159 optimal weight: 0.3980 chunk 128 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 95 optimal weight: 0.2980 chunk 167 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 250 GLN ** A 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 716 ASN A 917 ASN ** B 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 ASN ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 17373 Z= 0.220 Angle : 0.550 7.882 23787 Z= 0.293 Chirality : 0.041 0.184 2697 Planarity : 0.004 0.055 2755 Dihedral : 18.167 162.127 2893 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.26 % Allowed : 15.89 % Favored : 80.86 % 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: -0.16 (0.19), residues: 1894 helix: 0.67 (0.18), residues: 819 sheet: -0.81 (0.27), residues: 348 loop : -0.47 (0.22), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 470 HIS 0.005 0.001 HIS A 839 PHE 0.014 0.001 PHE B 410 TYR 0.023 0.002 TYR A 300 ARG 0.007 0.000 ARG A 823 *********************** 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 245 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 188 time to evaluate : 2.184 Fit side-chains revert: symmetry clash outliers start: 57 outliers final: 29 residues processed: 235 average time/residue: 1.0891 time to fit residues: 294.3373 Evaluate side-chains 202 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 173 time to evaluate : 2.104 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 29 residues processed: 0 time to fit residues: 2.8592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 62 optimal weight: 0.5980 chunk 168 optimal weight: 0.1980 chunk 36 optimal weight: 0.7980 chunk 109 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 186 optimal weight: 10.0000 chunk 155 optimal weight: 2.9990 chunk 86 optimal weight: 8.9990 chunk 15 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 ** 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: 0.7349 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 17373 Z= 0.248 Angle : 0.554 7.985 23787 Z= 0.294 Chirality : 0.041 0.176 2697 Planarity : 0.004 0.053 2755 Dihedral : 18.134 162.005 2893 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.43 % Allowed : 16.86 % Favored : 79.71 % 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: -0.08 (0.19), residues: 1894 helix: 0.75 (0.18), residues: 818 sheet: -0.79 (0.27), residues: 337 loop : -0.44 (0.22), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 470 HIS 0.004 0.001 HIS A 839 PHE 0.021 0.002 PHE A 992 TYR 0.028 0.002 TYR A 300 ARG 0.004 0.000 ARG A 223 *********************** 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 251 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 191 time to evaluate : 1.860 Fit side-chains revert: symmetry clash outliers start: 60 outliers final: 35 residues processed: 238 average time/residue: 1.0261 time to fit residues: 281.7369 Evaluate side-chains 214 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 179 time to evaluate : 1.894 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 30 residues processed: 5 average time/residue: 0.6944 time to fit residues: 6.7202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.3980 chunk 106 optimal weight: 8.9990 chunk 136 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 104 optimal weight: 0.6980 chunk 186 optimal weight: 10.0000 chunk 116 optimal weight: 8.9990 chunk 113 optimal weight: 8.9990 chunk 85 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 17373 Z= 0.324 Angle : 0.599 9.613 23787 Z= 0.316 Chirality : 0.043 0.177 2697 Planarity : 0.004 0.053 2755 Dihedral : 18.283 162.927 2893 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 17.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.49 % Allowed : 16.97 % Favored : 79.54 % 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: -0.10 (0.19), residues: 1894 helix: 0.67 (0.18), residues: 823 sheet: -0.79 (0.28), residues: 330 loop : -0.39 (0.22), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 89 HIS 0.004 0.001 HIS A 839 PHE 0.019 0.002 PHE A 992 TYR 0.031 0.002 TYR A 300 ARG 0.004 0.000 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: 61 poor density : 191 time to evaluate : 2.042 Fit side-chains outliers start: 61 outliers final: 31 residues processed: 234 average time/residue: 1.1367 time to fit residues: 305.5639 Evaluate side-chains 208 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 177 time to evaluate : 1.916 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 26 residues processed: 5 average time/residue: 0.2256 time to fit residues: 4.4474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 115 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 118 optimal weight: 9.9990 chunk 126 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 17 optimal weight: 0.1980 chunk 146 optimal weight: 0.7980 chunk 169 optimal weight: 9.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 17373 Z= 0.242 Angle : 0.565 8.698 23787 Z= 0.299 Chirality : 0.041 0.168 2697 Planarity : 0.004 0.052 2755 Dihedral : 18.154 162.921 2893 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.63 % Allowed : 18.51 % Favored : 78.86 % 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: 0.07 (0.19), residues: 1894 helix: 0.83 (0.18), residues: 819 sheet: -0.77 (0.28), residues: 326 loop : -0.28 (0.22), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 470 HIS 0.004 0.001 HIS A 839 PHE 0.030 0.002 PHE A 880 TYR 0.036 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 235 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 189 time to evaluate : 1.898 Fit side-chains outliers start: 46 outliers final: 28 residues processed: 223 average time/residue: 1.0817 time to fit residues: 277.8861 Evaluate side-chains 206 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 178 time to evaluate : 2.062 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 25 residues processed: 3 average time/residue: 0.6152 time to fit residues: 5.0562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 178 optimal weight: 0.7980 chunk 162 optimal weight: 0.9990 chunk 173 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 156 optimal weight: 0.9990 chunk 163 optimal weight: 0.5980 chunk 172 optimal weight: 0.6980 chunk 113 optimal weight: 8.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 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 151 HIS ** 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: 0.7363 moved from start: 0.3774 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= 0.243 Angle : 0.567 8.702 23787 Z= 0.299 Chirality : 0.041 0.172 2697 Planarity : 0.004 0.052 2755 Dihedral : 18.111 162.962 2893 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.91 % Allowed : 18.34 % Favored : 78.74 % 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: 0.84 (0.18), residues: 819 sheet: -0.81 (0.28), residues: 335 loop : -0.23 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 470 HIS 0.004 0.001 HIS A 839 PHE 0.025 0.002 PHE A 880 TYR 0.034 0.002 TYR A 300 ARG 0.006 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 236 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 185 time to evaluate : 2.036 Fit side-chains outliers start: 51 outliers final: 31 residues processed: 224 average time/residue: 1.0070 time to fit residues: 261.0888 Evaluate side-chains 209 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 178 time to evaluate : 1.910 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 25 residues processed: 6 average time/residue: 1.0684 time to fit residues: 9.8939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 183 optimal weight: 10.0000 chunk 111 optimal weight: 0.9980 chunk 86 optimal weight: 7.9990 chunk 127 optimal weight: 1.9990 chunk 192 optimal weight: 10.0000 chunk 176 optimal weight: 5.9990 chunk 153 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 118 optimal weight: 9.9990 chunk 93 optimal weight: 0.8980 chunk 121 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 17373 Z= 0.327 Angle : 0.617 11.181 23787 Z= 0.323 Chirality : 0.043 0.174 2697 Planarity : 0.004 0.052 2755 Dihedral : 18.292 163.401 2893 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 18.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.06 % Allowed : 19.71 % Favored : 78.23 % 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: 1894 helix: 0.72 (0.18), residues: 818 sheet: -0.84 (0.28), residues: 340 loop : -0.32 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 89 HIS 0.004 0.001 HIS A 839 PHE 0.022 0.002 PHE A 880 TYR 0.040 0.002 TYR A 300 ARG 0.006 0.000 ARG C 58 ********************** 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 219 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 183 time to evaluate : 2.049 Fit side-chains outliers start: 36 outliers final: 24 residues processed: 212 average time/residue: 1.0684 time to fit residues: 261.5041 Evaluate side-chains 198 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 174 time to evaluate : 1.941 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 22 residues processed: 2 average time/residue: 0.9522 time to fit residues: 4.8396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 163 optimal weight: 0.5980 chunk 46 optimal weight: 0.9980 chunk 141 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 153 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 134 optimal weight: 7.9990 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 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** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.181472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.150956 restraints weight = 18608.116| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 1.25 r_work: 0.3404 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3963 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= 0.239 Angle : 0.579 9.252 23787 Z= 0.304 Chirality : 0.041 0.170 2697 Planarity : 0.004 0.052 2755 Dihedral : 18.138 163.526 2893 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 17.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.00 % Allowed : 19.94 % Favored : 78.06 % 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: 0.02 (0.19), residues: 1894 helix: 0.82 (0.18), residues: 819 sheet: -0.85 (0.29), residues: 316 loop : -0.34 (0.22), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 470 HIS 0.004 0.001 HIS B -7 PHE 0.024 0.002 PHE A 880 TYR 0.038 0.002 TYR A 300 ARG 0.006 0.000 ARG C 193 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5185.68 seconds wall clock time: 94 minutes 44.78 seconds (5684.78 seconds total)