Starting phenix.real_space_refine on Tue Aug 6 13:51:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpp_37722/08_2024/8wpp_37722.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpp_37722/08_2024/8wpp_37722.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpp_37722/08_2024/8wpp_37722.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpp_37722/08_2024/8wpp_37722.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpp_37722/08_2024/8wpp_37722.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wpp_37722/08_2024/8wpp_37722.cif" } resolution = 3.1 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: 5 Type Number sf(0) Gaussians P 69 5.49 5 S 77 5.16 5 C 10515 2.51 5 N 2830 2.21 5 O 3335 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 GLU 45": "OE1" <-> "OE2" Residue "A PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 69": "OD1" <-> "OD2" Residue "A ASP 77": "OD1" <-> "OD2" Residue "A TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 166": "OD1" <-> "OD2" Residue "A GLU 206": "OE1" <-> "OE2" Residue "A ASP 268": "OD1" <-> "OD2" Residue "A GLU 512": "OE1" <-> "OE2" Residue "A PHE 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 528": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 723": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 743": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 914": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 930": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 968": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 179": "OE1" <-> "OE2" Residue "B TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 249": "OD1" <-> "OD2" Residue "B PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 380": "OE1" <-> "OE2" Residue "B PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 32": "OE1" <-> "OE2" Residue "C ASP 40": "OD1" <-> "OD2" Residue "C GLU 41": "OE1" <-> "OE2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "C GLU 129": "OE1" <-> "OE2" Residue "C ASP 186": "OD1" <-> "OD2" Residue "C ASP 205": "OD1" <-> "OD2" Residue "D ASP 147": "OD1" <-> "OD2" Residue "E PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 16826 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 8223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 8223 Classifications: {'peptide': 1006} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 37, 'TRANS': 968} Chain: "B" Number of atoms: 3557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 437, 3557 Classifications: {'peptide': 437} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 426} Chain: "C" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1773 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 204} Chain: "D" Number of atoms: 525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 525 Classifications: {'peptide': 69} Link IDs: {'TRANS': 68} Chain: "E" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 425 Classifications: {'peptide': 57} Link IDs: {'TRANS': 56} Chain: "F" Number of atoms: 481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 481 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 64} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 425 Classifications: {'peptide': 57} Link IDs: {'TRANS': 56} Chain: "H" Number of atoms: 639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 639 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "I" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 778 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Time building chain proxies: 9.19, per 1000 atoms: 0.55 Number of scatterers: 16826 At special positions: 0 Unit cell: (108.73, 136.12, 144.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 77 16.00 P 69 15.00 O 3335 8.00 N 2830 7.00 C 10515 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: 6.61 Conformation dependent library (CDL) restraints added in 2.8 seconds 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3656 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 19 sheets defined 46.4% alpha, 18.9% beta 31 base pairs and 56 stacking pairs defined. Time for finding SS restraints: 5.77 Creating SS restraints... Processing helix chain 'A' and resid 44 through 50 Processing helix chain 'A' and resid 108 through 117 removed outlier: 3.505A pdb=" N SER A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN A 117 " --> pdb=" O PHE A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 149 Processing helix chain 'A' and resid 209 through 219 Processing helix chain 'A' and resid 240 through 254 Processing helix chain 'A' and resid 267 through 280 Processing helix chain 'A' and resid 331 through 339 Processing helix chain 'A' and resid 345 through 354 Processing helix chain 'A' and resid 380 through 390 Processing helix chain 'A' and resid 439 through 446 Processing helix chain 'A' and resid 448 through 474 removed outlier: 3.665A pdb=" N GLN A 467 " --> pdb=" O ALA A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 486 Processing helix chain 'A' and resid 489 through 493 removed outlier: 3.802A pdb=" N VAL A 493 " --> pdb=" O GLN A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 514 removed outlier: 3.856A 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 552 through 562 Processing helix chain 'A' and resid 576 through 591 Processing helix chain 'A' and resid 621 through 643 Processing helix chain 'A' and resid 646 through 673 removed outlier: 4.314A pdb=" N TYR A 668 " --> pdb=" O ALA A 664 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLY A 669 " --> pdb=" O ASN A 665 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY A 672 " --> pdb=" O TYR A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 703 Processing helix chain 'A' and resid 763 through 781 Processing helix chain 'A' and resid 836 through 857 removed outlier: 3.501A pdb=" N GLY A 857 " --> pdb=" O MET A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 883 removed outlier: 3.727A pdb=" N VAL A 864 " --> pdb=" O ASN A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 891 removed outlier: 3.658A pdb=" N MET A 891 " --> pdb=" O GLU A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 918 Processing helix chain 'A' and resid 947 through 949 No H-bonds generated for 'chain 'A' and resid 947 through 949' Processing helix chain 'A' and resid 967 through 983 removed outlier: 4.337A pdb=" N TYR A 971 " --> pdb=" O PHE A 967 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 982 " --> pdb=" O GLU A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 997 removed outlier: 4.092A pdb=" N CYS A 989 " --> pdb=" O ASN A 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 19 Processing helix chain 'B' and resid 24 through 43 Processing helix chain 'B' and resid 57 through 61 Processing helix chain 'B' and resid 107 through 121 Processing helix chain 'B' and resid 147 through 158 removed outlier: 4.294A pdb=" N ILE B 151 " --> pdb=" O SER B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 189 Processing helix chain 'B' and resid 249 through 256 removed outlier: 3.579A pdb=" N SER B 256 " --> pdb=" O HIS B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 298 Processing helix chain 'B' and resid 315 through 323 removed outlier: 4.296A pdb=" N LEU B 319 " --> pdb=" O GLY B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 341 removed outlier: 3.677A pdb=" N LEU B 334 " --> pdb=" O THR B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 351 Processing helix chain 'B' and resid 352 through 361 removed outlier: 3.657A pdb=" N LEU B 361 " --> pdb=" O SER B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 373 Processing helix chain 'B' and resid 391 through 395 removed outlier: 3.919A pdb=" N CYS B 394 " --> pdb=" O ASN B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 406 Processing helix chain 'B' and resid 406 through 426 Processing helix chain 'C' and resid 16 through 21 removed outlier: 3.509A pdb=" N GLU C 20 " --> pdb=" O ASP C 17 " (cutoff:3.500A) Proline residue: C 21 - end of helix Processing helix chain 'C' and resid 22 through 38 removed outlier: 3.797A pdb=" N GLU C 32 " --> pdb=" O GLU C 28 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N SER C 35 " --> pdb=" O ASN C 31 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N TRP C 36 " --> pdb=" O GLU C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 49 removed outlier: 3.698A pdb=" N PHE C 49 " --> pdb=" O PRO C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 55 Processing helix chain 'C' and resid 86 through 101 Processing helix chain 'C' and resid 133 through 152 removed outlier: 5.439A pdb=" N LYS C 139 " --> pdb=" O ILE C 135 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ILE C 140 " --> pdb=" O TYR C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 170 Processing helix chain 'C' and resid 187 through 192 Processing helix chain 'C' and resid 193 through 205 Processing helix chain 'C' and resid 211 through 214 Processing helix chain 'D' and resid 142 through 174 removed outlier: 3.583A pdb=" N ASP D 169 " --> pdb=" O THR D 165 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY D 174 " --> pdb=" O VAL D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 198 Processing helix chain 'E' and resid 141 through 164 Processing helix chain 'E' and resid 168 through 196 Processing helix chain 'F' and resid 142 through 173 removed outlier: 4.025A pdb=" N LEU F 153 " --> pdb=" O ILE F 149 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS F 155 " --> pdb=" O LYS F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 200 Processing helix chain 'G' and resid 141 through 164 Processing helix chain 'G' and resid 168 through 195 Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 136 removed outlier: 7.081A pdb=" N CYS A 139 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ARG A 23 " --> pdb=" O CYS A 5 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N CYS A 5 " --> pdb=" O ARG A 23 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N CYS A 124 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LYS A 151 " --> pdb=" O SER A 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 43 removed outlier: 6.161A pdb=" N SER A 84 " --> pdb=" O ARG A 64 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ARG A 64 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ALA A 86 " --> pdb=" O LYS A 62 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LYS A 62 " --> pdb=" O ALA A 86 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N MET A 88 " --> pdb=" O MET A 60 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG A 58 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN A 56 " --> pdb=" O GLU A 92 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 72 through 73 removed outlier: 6.317A pdb=" N LEU A 568 " --> pdb=" O ASP A 616 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ASP A 616 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLY A 570 " --> pdb=" O ILE A 614 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER A 610 " --> pdb=" O SER A 574 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU A 611 " --> pdb=" O CYS A 601 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 222 through 223 removed outlier: 6.581A pdb=" N LEU A 222 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N SER A 184 " --> pdb=" O ASN A 204 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N VAL A 259 " --> pdb=" O PHE A 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 285 through 287 Processing sheet with id=AA6, first strand: chain 'A' and resid 299 through 305 Processing sheet with id=AA7, first strand: chain 'A' and resid 355 through 362 removed outlier: 3.677A pdb=" N LEU A 361 " --> pdb=" O THR A 369 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N THR A 369 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY A 372 " --> pdb=" O PHE A 415 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ARG A 407 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N SER A 420 " --> pdb=" O VAL A 405 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N VAL A 405 " --> pdb=" O SER A 420 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 732 through 734 removed outlier: 6.916A pdb=" N PHE A 756 " --> pdb=" O VAL A 748 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N GLY A 750 " --> pdb=" O SER A 754 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N SER A 754 " --> pdb=" O GLY A 750 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N VAL A 545 " --> pdb=" O VAL A 794 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N VAL A 794 " --> pdb=" O VAL A 545 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ILE A 547 " --> pdb=" O GLU A 792 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N TYR A 795 " --> pdb=" O TYR A 811 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N TYR A 811 " --> pdb=" O TYR A 795 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ASN A 797 " --> pdb=" O MET A 809 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N MET A 809 " --> pdb=" O ASN A 797 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LYS A 805 " --> pdb=" O GLN A 801 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU A 822 " --> pdb=" O LYS A 810 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 892 through 895 Processing sheet with id=AB1, first strand: chain 'A' and resid 892 through 895 Processing sheet with id=AB2, first strand: chain 'B' and resid 69 through 70 removed outlier: 3.775A pdb=" N PHE B 69 " --> pdb=" O PHE B 176 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 166 through 167 removed outlier: 3.924A pdb=" N LEU B 166 " --> pdb=" O PHE B 78 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLN B 208 " --> pdb=" O TYR B 199 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 103 through 104 removed outlier: 4.275A pdb=" N MET B 95 " --> pdb=" O PHE B 104 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ARG B 128 " --> pdb=" O GLU B 139 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU B 132 " --> pdb=" O ARG B 135 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 220 through 227 Processing sheet with id=AB6, first strand: chain 'B' and resid 220 through 227 removed outlier: 3.528A pdb=" N VAL B 237 " --> pdb=" O ILE B 245 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N SER B 273 " --> pdb=" O LYS B 244 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL B 264 " --> pdb=" O MET B 218 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N MET B 218 " --> pdb=" O VAL B 264 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 375 through 379 Processing sheet with id=AB8, first strand: chain 'C' and resid 2 through 5 removed outlier: 3.518A pdb=" N ILE C 13 " --> pdb=" O VAL C 4 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 116 through 120 Processing sheet with id=AC1, first strand: chain 'C' and resid 107 through 108 821 hydrogen bonds defined for protein. 2391 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: 6.92 Time building geometry restraints manager: 7.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4079 1.33 - 1.46: 3945 1.46 - 1.58: 9016 1.58 - 1.70: 137 1.70 - 1.82: 120 Bond restraints: 17297 Sorted by residual: bond pdb=" CG PRO A 821 " pdb=" CD PRO A 821 " ideal model delta sigma weight residual 1.503 1.258 0.245 3.40e-02 8.65e+02 5.21e+01 bond pdb=" N PRO A 821 " pdb=" CD PRO A 821 " ideal model delta sigma weight residual 1.473 1.521 -0.048 1.40e-02 5.10e+03 1.19e+01 bond pdb=" CB PRO A 821 " pdb=" CG PRO A 821 " ideal model delta sigma weight residual 1.492 1.663 -0.171 5.00e-02 4.00e+02 1.17e+01 bond pdb=" C3' DA H 27 " pdb=" O3' DA H 27 " ideal model delta sigma weight residual 1.422 1.491 -0.069 3.00e-02 1.11e+03 5.34e+00 bond pdb=" CA PHE A 930 " pdb=" CB PHE A 930 " ideal model delta sigma weight residual 1.535 1.571 -0.036 1.93e-02 2.68e+03 3.42e+00 ... (remaining 17292 not shown) Histogram of bond angle deviations from ideal: 88.60 - 97.71: 2 97.71 - 106.82: 804 106.82 - 115.93: 10824 115.93 - 125.03: 11612 125.03 - 134.14: 428 Bond angle restraints: 23670 Sorted by residual: angle pdb=" CA PRO A 821 " pdb=" N PRO A 821 " pdb=" CD PRO A 821 " ideal model delta sigma weight residual 112.00 97.90 14.10 1.40e+00 5.10e-01 1.01e+02 angle pdb=" N PRO A 821 " pdb=" CD PRO A 821 " pdb=" CG PRO A 821 " ideal model delta sigma weight residual 103.20 88.60 14.60 1.50e+00 4.44e-01 9.47e+01 angle pdb=" CA PRO A 821 " pdb=" CB PRO A 821 " pdb=" CG PRO A 821 " ideal model delta sigma weight residual 104.50 94.33 10.17 1.90e+00 2.77e-01 2.86e+01 angle pdb=" N VAL D 200 " pdb=" CA VAL D 200 " pdb=" C VAL D 200 " ideal model delta sigma weight residual 113.71 109.54 4.17 9.50e-01 1.11e+00 1.92e+01 angle pdb=" CB MET B 95 " pdb=" CG MET B 95 " pdb=" SD MET B 95 " ideal model delta sigma weight residual 112.70 100.14 12.56 3.00e+00 1.11e-01 1.75e+01 ... (remaining 23665 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.52: 9725 30.52 - 61.04: 564 61.04 - 91.56: 21 91.56 - 122.08: 0 122.08 - 152.60: 1 Dihedral angle restraints: 10311 sinusoidal: 4660 harmonic: 5651 Sorted by residual: dihedral pdb=" CA GLU G 168 " pdb=" C GLU G 168 " pdb=" N ASP G 169 " pdb=" CA ASP G 169 " ideal model delta harmonic sigma weight residual -180.00 -146.00 -34.00 0 5.00e+00 4.00e-02 4.62e+01 dihedral pdb=" CA ARG A 497 " pdb=" C ARG A 497 " pdb=" N ALA A 498 " pdb=" CA ALA A 498 " ideal model delta harmonic sigma weight residual -180.00 -157.02 -22.98 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" CA HIS B -9 " pdb=" C HIS B -9 " pdb=" N HIS B -8 " pdb=" CA HIS B -8 " ideal model delta harmonic sigma weight residual 180.00 158.05 21.95 0 5.00e+00 4.00e-02 1.93e+01 ... (remaining 10308 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 2343 0.074 - 0.148: 305 0.148 - 0.222: 32 0.222 - 0.297: 2 0.297 - 0.371: 4 Chirality restraints: 2686 Sorted by residual: chirality pdb=" CB ILE C 117 " pdb=" CA ILE C 117 " pdb=" CG1 ILE C 117 " pdb=" CG2 ILE C 117 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.44e+00 chirality pdb=" CB VAL E 166 " pdb=" CA VAL E 166 " pdb=" CG1 VAL E 166 " pdb=" CG2 VAL E 166 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.23e+00 chirality pdb=" CB ILE B 45 " pdb=" CA ILE B 45 " pdb=" CG1 ILE B 45 " pdb=" CG2 ILE B 45 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.87e+00 ... (remaining 2683 not shown) Planarity restraints: 2755 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 820 " 0.107 5.00e-02 4.00e+02 1.48e-01 3.52e+01 pdb=" N PRO A 821 " -0.256 5.00e-02 4.00e+02 pdb=" CA PRO A 821 " 0.076 5.00e-02 4.00e+02 pdb=" CD PRO A 821 " 0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 930 " 0.017 2.00e-02 2.50e+03 2.42e-02 1.02e+01 pdb=" CG PHE A 930 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 PHE A 930 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE A 930 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 PHE A 930 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 930 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 930 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 668 " -0.023 2.00e-02 2.50e+03 1.78e-02 6.35e+00 pdb=" CG TYR A 668 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TYR A 668 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR A 668 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 668 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 668 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 668 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 668 " -0.001 2.00e-02 2.50e+03 ... (remaining 2752 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3082 2.78 - 3.31: 15354 3.31 - 3.84: 30760 3.84 - 4.37: 35467 4.37 - 4.90: 58403 Nonbonded interactions: 143066 Sorted by model distance: nonbonded pdb=" OH TYR A 162 " pdb=" OE1 GLU A 476 " model vdw 2.245 3.040 nonbonded pdb=" O SER F 161 " pdb=" OG1 THR F 165 " model vdw 2.305 3.040 nonbonded pdb=" OG SER C 153 " pdb=" OD2 ASP C 205 " model vdw 2.313 3.040 nonbonded pdb=" OH TYR B 89 " pdb=" OD1 ASN B 115 " model vdw 2.313 3.040 nonbonded pdb=" O PHE F 179 " pdb=" OG1 THR F 183 " model vdw 2.315 3.040 ... (remaining 143061 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 1.150 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: 0.690 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 50.170 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.060 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 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 : 0.005 0.245 17297 Z= 0.286 Angle : 0.842 14.597 23670 Z= 0.453 Chirality : 0.052 0.371 2686 Planarity : 0.007 0.148 2755 Dihedral : 16.997 152.597 6655 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.06 % Allowed : 0.23 % Favored : 99.71 % 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: -1.85 (0.17), residues: 1895 helix: -1.24 (0.15), residues: 833 sheet: -0.76 (0.28), residues: 322 loop : -1.20 (0.20), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP C 19 HIS 0.006 0.001 HIS A 319 PHE 0.055 0.002 PHE A 930 TYR 0.043 0.002 TYR A 668 ARG 0.017 0.001 ARG A 234 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 277 time to evaluate : 1.791 Fit side-chains REVERT: A 519 ARG cc_start: 0.7309 (mtt-85) cc_final: 0.7080 (mtt90) REVERT: B 263 PHE cc_start: 0.7240 (m-80) cc_final: 0.7008 (m-80) REVERT: C 55 GLN cc_start: 0.7885 (OUTLIER) cc_final: 0.6724 (mm110) REVERT: C 58 ARG cc_start: 0.6720 (mpt-90) cc_final: 0.6304 (mmt180) REVERT: D 182 MET cc_start: 0.4629 (mmp) cc_final: 0.3948 (ptm) outliers start: 1 outliers final: 0 residues processed: 277 average time/residue: 0.2804 time to fit residues: 118.1041 Evaluate side-chains 206 residues out of total 1753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 205 time to evaluate : 1.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 55 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 0.9980 chunk 145 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 112 optimal weight: 5.9990 chunk 174 optimal weight: 10.0000 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 HIS ** A 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 147 ASN A 336 GLN A 426 ASN A 543 ASN A 785 ASN A 825 ASN ** B -9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17297 Z= 0.242 Angle : 0.572 7.881 23670 Z= 0.315 Chirality : 0.042 0.170 2686 Planarity : 0.005 0.057 2755 Dihedral : 17.533 155.158 2854 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.69 % Allowed : 7.60 % Favored : 91.72 % 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: -0.85 (0.18), residues: 1895 helix: 0.07 (0.17), residues: 829 sheet: -0.98 (0.27), residues: 317 loop : -0.93 (0.21), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 136 HIS 0.006 0.001 HIS A 185 PHE 0.026 0.002 PHE A 791 TYR 0.019 0.001 TYR A 668 ARG 0.009 0.001 ARG B 135 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 224 time to evaluate : 1.966 Fit side-chains REVERT: A 674 ARG cc_start: 0.8076 (ttm-80) cc_final: 0.7781 (ttm110) REVERT: B 138 MET cc_start: 0.8023 (ttp) cc_final: 0.7715 (ttp) REVERT: C 58 ARG cc_start: 0.6878 (mpt-90) cc_final: 0.6482 (mmt180) REVERT: D 182 MET cc_start: 0.4265 (mmp) cc_final: 0.3663 (ptm) outliers start: 12 outliers final: 8 residues processed: 230 average time/residue: 0.2756 time to fit residues: 98.5937 Evaluate side-chains 197 residues out of total 1753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 189 time to evaluate : 1.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 250 GLN Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 767 SER Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 344 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 145 optimal weight: 0.0980 chunk 118 optimal weight: 9.9990 chunk 48 optimal weight: 0.9980 chunk 174 optimal weight: 20.0000 chunk 188 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 173 optimal weight: 0.6980 chunk 59 optimal weight: 0.2980 chunk 140 optimal weight: 3.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN A 538 GLN ** B -9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 ASN B 351 GLN ** B 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 ASN C 55 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17297 Z= 0.273 Angle : 0.566 9.120 23670 Z= 0.309 Chirality : 0.042 0.161 2686 Planarity : 0.004 0.048 2755 Dihedral : 17.589 158.165 2851 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.20 % Allowed : 9.99 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.18), residues: 1895 helix: 0.51 (0.17), residues: 831 sheet: -1.18 (0.27), residues: 323 loop : -0.79 (0.22), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 136 HIS 0.004 0.001 HIS C 8 PHE 0.019 0.002 PHE A 433 TYR 0.022 0.002 TYR A 668 ARG 0.005 0.000 ARG A 234 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 196 time to evaluate : 1.949 Fit side-chains revert: symmetry clash REVERT: A 711 MET cc_start: 0.7260 (ttt) cc_final: 0.7037 (ttt) REVERT: B 137 ILE cc_start: 0.8583 (pt) cc_final: 0.8356 (tt) REVERT: B 208 GLN cc_start: 0.6370 (mp-120) cc_final: 0.5916 (mp10) REVERT: C 58 ARG cc_start: 0.6892 (mpt-90) cc_final: 0.6538 (mmt180) REVERT: D 182 MET cc_start: 0.4408 (mmp) cc_final: 0.3898 (ptm) outliers start: 21 outliers final: 15 residues processed: 208 average time/residue: 0.2900 time to fit residues: 93.1103 Evaluate side-chains 197 residues out of total 1753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 182 time to evaluate : 1.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 250 GLN Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 864 VAL Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain D residue 153 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 172 optimal weight: 9.9990 chunk 131 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 83 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 175 optimal weight: 8.9990 chunk 185 optimal weight: 10.0000 chunk 91 optimal weight: 0.0980 chunk 166 optimal weight: 6.9990 chunk 50 optimal weight: 0.9980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN ** B -9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN B 122 ASN ** B 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 55 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 17297 Z= 0.355 Angle : 0.602 8.521 23670 Z= 0.325 Chirality : 0.043 0.184 2686 Planarity : 0.004 0.051 2755 Dihedral : 17.712 160.006 2851 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.66 % Allowed : 11.31 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.19), residues: 1895 helix: 0.65 (0.17), residues: 825 sheet: -1.34 (0.27), residues: 331 loop : -0.76 (0.22), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 8 HIS 0.006 0.001 HIS C 133 PHE 0.017 0.002 PHE A 267 TYR 0.038 0.002 TYR A 668 ARG 0.006 0.000 ARG A 519 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 197 time to evaluate : 1.846 Fit side-chains REVERT: A 165 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8281 (pp) REVERT: A 711 MET cc_start: 0.7382 (ttt) cc_final: 0.7164 (ttt) REVERT: C 58 ARG cc_start: 0.6960 (mpt-90) cc_final: 0.6539 (mmt180) REVERT: D 182 MET cc_start: 0.4464 (mmp) cc_final: 0.3983 (ptm) outliers start: 29 outliers final: 17 residues processed: 218 average time/residue: 0.2891 time to fit residues: 98.0362 Evaluate side-chains 192 residues out of total 1753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 174 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 250 GLN Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 204 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 154 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 138 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 158 optimal weight: 0.5980 chunk 128 optimal weight: 3.9990 chunk 0 optimal weight: 0.5980 chunk 94 optimal weight: 0.0170 chunk 166 optimal weight: 6.9990 chunk 46 optimal weight: 0.6980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN ** A 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 170 HIS ** B -9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 ASN C 55 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17297 Z= 0.189 Angle : 0.530 9.564 23670 Z= 0.288 Chirality : 0.041 0.249 2686 Planarity : 0.004 0.046 2755 Dihedral : 17.523 157.965 2851 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.66 % Allowed : 12.91 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.19), residues: 1895 helix: 0.94 (0.17), residues: 828 sheet: -1.23 (0.27), residues: 327 loop : -0.61 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 470 HIS 0.004 0.001 HIS C 133 PHE 0.025 0.001 PHE A 791 TYR 0.020 0.001 TYR A 668 ARG 0.006 0.000 ARG B 423 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 207 time to evaluate : 1.821 Fit side-chains revert: symmetry clash REVERT: A 181 ASN cc_start: 0.6937 (m-40) cc_final: 0.6621 (m-40) REVERT: C 58 ARG cc_start: 0.6857 (mpt-90) cc_final: 0.6541 (mmt180) REVERT: D 182 MET cc_start: 0.4406 (mmp) cc_final: 0.3958 (ptm) outliers start: 29 outliers final: 17 residues processed: 224 average time/residue: 0.2845 time to fit residues: 98.2287 Evaluate side-chains 203 residues out of total 1753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 186 time to evaluate : 1.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 250 GLN Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain C residue 152 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 62 optimal weight: 0.9980 chunk 167 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 108 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 185 optimal weight: 5.9990 chunk 154 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN ** A 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN A 426 ASN ** B -9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 ASN C 55 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17297 Z= 0.226 Angle : 0.539 10.128 23670 Z= 0.291 Chirality : 0.041 0.245 2686 Planarity : 0.004 0.044 2755 Dihedral : 17.526 158.348 2851 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.71 % Allowed : 13.42 % Favored : 84.87 % 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: 1895 helix: 1.00 (0.17), residues: 836 sheet: -1.25 (0.28), residues: 320 loop : -0.56 (0.22), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 136 HIS 0.004 0.001 HIS C 133 PHE 0.023 0.001 PHE A 838 TYR 0.021 0.001 TYR A 668 ARG 0.005 0.000 ARG B 423 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 196 time to evaluate : 1.825 Fit side-chains REVERT: A 181 ASN cc_start: 0.6917 (m-40) cc_final: 0.6622 (m-40) REVERT: A 268 ASP cc_start: 0.8050 (m-30) cc_final: 0.7594 (m-30) REVERT: A 345 LYS cc_start: 0.8148 (OUTLIER) cc_final: 0.7719 (ptpt) REVERT: B 218 MET cc_start: 0.7070 (mtt) cc_final: 0.6796 (mtp) REVERT: B 424 LEU cc_start: 0.6921 (OUTLIER) cc_final: 0.6578 (mp) REVERT: C 58 ARG cc_start: 0.6871 (mpt-90) cc_final: 0.6561 (mmt180) REVERT: D 182 MET cc_start: 0.4432 (mmp) cc_final: 0.4006 (ptm) outliers start: 30 outliers final: 18 residues processed: 217 average time/residue: 0.2592 time to fit residues: 89.1297 Evaluate side-chains 208 residues out of total 1753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 188 time to evaluate : 1.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 250 GLN Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain C residue 152 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 179 optimal weight: 8.9990 chunk 20 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 135 optimal weight: 8.9990 chunk 156 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 185 optimal weight: 5.9990 chunk 115 optimal weight: 0.0060 chunk 112 optimal weight: 10.0000 chunk 85 optimal weight: 0.4980 chunk 114 optimal weight: 0.9980 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN ** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B -9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 ASN C 55 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17297 Z= 0.230 Angle : 0.543 10.256 23670 Z= 0.294 Chirality : 0.041 0.171 2686 Planarity : 0.004 0.044 2755 Dihedral : 17.516 157.990 2851 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.06 % Allowed : 13.48 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.19), residues: 1895 helix: 1.00 (0.17), residues: 840 sheet: -1.28 (0.28), residues: 327 loop : -0.50 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 8 HIS 0.004 0.001 HIS C 133 PHE 0.021 0.001 PHE A 838 TYR 0.022 0.001 TYR A 668 ARG 0.005 0.000 ARG C 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 198 time to evaluate : 2.094 Fit side-chains REVERT: A 181 ASN cc_start: 0.6923 (m-40) cc_final: 0.6671 (m-40) REVERT: A 345 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7713 (ptpt) REVERT: B 424 LEU cc_start: 0.6925 (OUTLIER) cc_final: 0.6591 (mp) REVERT: C 58 ARG cc_start: 0.6875 (mpt-90) cc_final: 0.6573 (mmt180) REVERT: D 182 MET cc_start: 0.4454 (mmp) cc_final: 0.4043 (ptm) outliers start: 36 outliers final: 22 residues processed: 217 average time/residue: 0.2652 time to fit residues: 91.4377 Evaluate side-chains 210 residues out of total 1753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 186 time to evaluate : 1.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 250 GLN Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 152 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 0.0270 chunk 110 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 36 optimal weight: 0.0770 chunk 35 optimal weight: 0.5980 chunk 117 optimal weight: 9.9990 chunk 126 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 17 optimal weight: 0.0470 chunk 145 optimal weight: 0.4980 chunk 168 optimal weight: 0.0970 overall best weight: 0.1492 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B -9 HIS B 122 ASN C 55 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17297 Z= 0.153 Angle : 0.520 9.937 23670 Z= 0.281 Chirality : 0.040 0.215 2686 Planarity : 0.004 0.044 2755 Dihedral : 17.349 155.453 2851 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.48 % Allowed : 14.51 % Favored : 84.01 % 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: 1895 helix: 1.22 (0.18), residues: 840 sheet: -1.01 (0.29), residues: 322 loop : -0.46 (0.23), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 470 HIS 0.004 0.001 HIS B 252 PHE 0.020 0.001 PHE A 838 TYR 0.018 0.001 TYR A 668 ARG 0.006 0.000 ARG C 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 210 time to evaluate : 1.812 Fit side-chains revert: symmetry clash REVERT: A 165 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8183 (pp) REVERT: A 357 MET cc_start: 0.7438 (mmp) cc_final: 0.7220 (mmp) REVERT: B 424 LEU cc_start: 0.6878 (OUTLIER) cc_final: 0.6583 (mp) REVERT: C 58 ARG cc_start: 0.6865 (mpt-90) cc_final: 0.6617 (mmt180) REVERT: D 182 MET cc_start: 0.4498 (mmp) cc_final: 0.4123 (ptm) outliers start: 26 outliers final: 13 residues processed: 221 average time/residue: 0.2770 time to fit residues: 94.8895 Evaluate side-chains 206 residues out of total 1753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 191 time to evaluate : 1.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 526 PHE Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain C residue 152 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 177 optimal weight: 6.9990 chunk 161 optimal weight: 2.9990 chunk 172 optimal weight: 9.9990 chunk 103 optimal weight: 7.9990 chunk 75 optimal weight: 4.9990 chunk 135 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 chunk 163 optimal weight: 0.7980 chunk 171 optimal weight: 3.9990 chunk 113 optimal weight: 9.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 576 ASN ** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 55 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 17297 Z= 0.450 Angle : 0.654 11.060 23670 Z= 0.348 Chirality : 0.046 0.204 2686 Planarity : 0.005 0.044 2755 Dihedral : 17.738 160.123 2851 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.60 % Allowed : 14.91 % Favored : 83.50 % 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: -0.14 (0.19), residues: 1895 helix: 0.91 (0.17), residues: 833 sheet: -1.17 (0.27), residues: 346 loop : -0.57 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 8 HIS 0.007 0.002 HIS A 36 PHE 0.022 0.002 PHE B 387 TYR 0.024 0.002 TYR A 668 ARG 0.009 0.001 ARG C 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 188 time to evaluate : 1.976 Fit side-chains REVERT: A 165 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8397 (pp) REVERT: B 424 LEU cc_start: 0.7103 (OUTLIER) cc_final: 0.6733 (mp) REVERT: C 58 ARG cc_start: 0.6890 (mpt-90) cc_final: 0.6640 (mmt180) REVERT: D 182 MET cc_start: 0.4577 (mmp) cc_final: 0.4197 (ptm) outliers start: 28 outliers final: 19 residues processed: 206 average time/residue: 0.2940 time to fit residues: 93.5193 Evaluate side-chains 199 residues out of total 1753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 178 time to evaluate : 1.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 55 GLN Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain G residue 166 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 182 optimal weight: 10.0000 chunk 111 optimal weight: 6.9990 chunk 86 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 chunk 191 optimal weight: 20.0000 chunk 176 optimal weight: 5.9990 chunk 152 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 117 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 120 optimal weight: 7.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 55 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 17297 Z= 0.378 Angle : 0.635 11.111 23670 Z= 0.338 Chirality : 0.045 0.236 2686 Planarity : 0.004 0.055 2755 Dihedral : 17.743 158.557 2851 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.48 % Allowed : 15.71 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.19), residues: 1895 helix: 0.79 (0.17), residues: 841 sheet: -1.20 (0.27), residues: 323 loop : -0.73 (0.23), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 8 HIS 0.006 0.001 HIS C 133 PHE 0.023 0.002 PHE B 233 TYR 0.024 0.002 TYR A 668 ARG 0.009 0.001 ARG B 286 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 179 time to evaluate : 1.811 Fit side-chains REVERT: A 165 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8356 (pp) REVERT: A 345 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7868 (ptpt) REVERT: A 566 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6890 (pm20) REVERT: B 424 LEU cc_start: 0.7031 (OUTLIER) cc_final: 0.6702 (mp) REVERT: C 58 ARG cc_start: 0.6836 (mpt-90) cc_final: 0.6606 (mmt180) REVERT: D 182 MET cc_start: 0.4628 (mmp) cc_final: 0.4277 (ptm) outliers start: 26 outliers final: 18 residues processed: 198 average time/residue: 0.2942 time to fit residues: 90.0720 Evaluate side-chains 190 residues out of total 1753 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 168 time to evaluate : 1.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 172 ASP Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 566 GLU Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain G residue 166 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 140 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 152 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 156 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 133 optimal weight: 5.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 55 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.210052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.166624 restraints weight = 18386.639| |-----------------------------------------------------------------------------| r_work (start): 0.3884 rms_B_bonded: 3.07 r_work: 0.3376 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 17297 Z= 0.268 Angle : 0.595 10.921 23670 Z= 0.318 Chirality : 0.043 0.180 2686 Planarity : 0.004 0.042 2755 Dihedral : 17.667 158.530 2851 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.37 % Allowed : 15.99 % Favored : 82.64 % 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: 1895 helix: 0.97 (0.17), residues: 838 sheet: -1.21 (0.28), residues: 314 loop : -0.58 (0.23), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 8 HIS 0.005 0.001 HIS C 133 PHE 0.016 0.002 PHE A 526 TYR 0.023 0.002 TYR A 668 ARG 0.009 0.000 ARG C 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3436.69 seconds wall clock time: 62 minutes 33.35 seconds (3753.35 seconds total)