Starting phenix.real_space_refine on Sun Apr 7 21:04:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8otw_17185/04_2024/8otw_17185_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8otw_17185/04_2024/8otw_17185.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8otw_17185/04_2024/8otw_17185.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8otw_17185/04_2024/8otw_17185.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8otw_17185/04_2024/8otw_17185_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8otw_17185/04_2024/8otw_17185_updated.pdb" } resolution = 3.68 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= 0.012 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 2 5.49 5 S 60 5.16 5 C 7525 2.51 5 N 1935 2.21 5 O 2049 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 219": "OD1" <-> "OD2" Residue "B GLU 337": "OE1" <-> "OE2" Residue "B GLU 616": "OE1" <-> "OE2" Residue "A PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 300": "OE1" <-> "OE2" Residue "A PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 449": "OD1" <-> "OD2" Residue "A GLU 503": "OE1" <-> "OE2" Residue "A GLU 531": "OE1" <-> "OE2" Residue "A TYR 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 606": "OE1" <-> "OE2" Residue "A ASP 838": "OD1" <-> "OD2" Residue "A GLU 935": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 11571 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 6102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 833, 6102 Classifications: {'peptide': 833} Incomplete info: {'truncation_to_alanine': 127} Link IDs: {'PTRANS': 25, 'TRANS': 807} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 460 Unresolved non-hydrogen angles: 586 Unresolved non-hydrogen dihedrals: 381 Unresolved non-hydrogen chiralities: 58 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 6, 'TYR:plan': 5, 'ASN:plan1': 5, 'TRP:plan': 1, 'HIS:plan': 4, 'PHE:plan': 7, 'GLU:plan': 6, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 195 Chain: "A" Number of atoms: 5383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 689, 5383 Classifications: {'peptide': 689} Link IDs: {'PTRANS': 20, 'TRANS': 668} Chain breaks: 2 Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Time building chain proxies: 6.78, per 1000 atoms: 0.59 Number of scatterers: 11571 At special positions: 0 Unit cell: (102.66, 133.558, 107.644, 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 60 16.00 P 2 15.00 O 2049 8.00 N 1935 7.00 C 7525 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: 5.02 Conformation dependent library (CDL) restraints added in 2.2 seconds 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2862 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 63 helices and 0 sheets defined 75.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.60 Creating SS restraints... Processing helix chain 'B' and resid 77 through 94 removed outlier: 4.362A pdb=" N ILE B 81 " --> pdb=" O VAL B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 119 removed outlier: 4.024A pdb=" N VAL B 115 " --> pdb=" O ALA B 111 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL B 116 " --> pdb=" O ILE B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 126 Processing helix chain 'B' and resid 128 through 131 No H-bonds generated for 'chain 'B' and resid 128 through 131' Processing helix chain 'B' and resid 135 through 139 Processing helix chain 'B' and resid 142 through 152 Processing helix chain 'B' and resid 156 through 187 removed outlier: 3.573A pdb=" N SER B 162 " --> pdb=" O THR B 158 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N SER B 164 " --> pdb=" O MET B 160 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLN B 165 " --> pdb=" O ARG B 161 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASN B 187 " --> pdb=" O VAL B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 205 Processing helix chain 'B' and resid 211 through 220 removed outlier: 3.603A pdb=" N LEU B 220 " --> pdb=" O LEU B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 253 removed outlier: 3.668A pdb=" N SER B 234 " --> pdb=" O ILE B 230 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL B 243 " --> pdb=" O GLY B 239 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N MET B 251 " --> pdb=" O VAL B 247 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N VAL B 252 " --> pdb=" O PHE B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 272 Processing helix chain 'B' and resid 274 through 292 removed outlier: 3.985A pdb=" N HIS B 292 " --> pdb=" O PHE B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 316 Processing helix chain 'B' and resid 324 through 336 Processing helix chain 'B' and resid 338 through 340 No H-bonds generated for 'chain 'B' and resid 338 through 340' Processing helix chain 'B' and resid 343 through 374 Processing helix chain 'B' and resid 382 through 412 removed outlier: 3.999A pdb=" N PHE B 386 " --> pdb=" O LYS B 382 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ARG B 399 " --> pdb=" O ILE B 395 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N GLY B 400 " --> pdb=" O THR B 396 " (cutoff:3.500A) Proline residue: B 408 - end of helix removed outlier: 3.546A pdb=" N ARG B 412 " --> pdb=" O PRO B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 427 Processing helix chain 'B' and resid 433 through 445 Processing helix chain 'B' and resid 453 through 481 removed outlier: 3.899A pdb=" N ALA B 471 " --> pdb=" O LEU B 467 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR B 472 " --> pdb=" O VAL B 468 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLN B 475 " --> pdb=" O ALA B 471 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N THR B 476 " --> pdb=" O THR B 472 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG B 479 " --> pdb=" O GLN B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 514 removed outlier: 4.425A pdb=" N SER B 514 " --> pdb=" O ASN B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 529 Processing helix chain 'B' and resid 574 through 599 removed outlier: 3.848A pdb=" N MET B 578 " --> pdb=" O GLU B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 620 Processing helix chain 'B' and resid 634 through 637 No H-bonds generated for 'chain 'B' and resid 634 through 637' Processing helix chain 'B' and resid 642 through 653 Processing helix chain 'B' and resid 669 through 676 Processing helix chain 'B' and resid 678 through 703 removed outlier: 4.077A pdb=" N VAL B 693 " --> pdb=" O VAL B 689 " (cutoff:3.500A) Proline residue: B 694 - end of helix Processing helix chain 'B' and resid 724 through 749 removed outlier: 3.898A pdb=" N ILE B 728 " --> pdb=" O SER B 724 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASP B 730 " --> pdb=" O GLN B 726 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU B 732 " --> pdb=" O ILE B 728 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N ARG B 733 " --> pdb=" O GLU B 729 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 760 Processing helix chain 'B' and resid 762 through 783 removed outlier: 4.401A pdb=" N ASP B 767 " --> pdb=" O TRP B 763 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ALA B 768 " --> pdb=" O ASN B 764 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N PHE B 769 " --> pdb=" O LYS B 765 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ILE B 770 " --> pdb=" O PHE B 766 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU B 771 " --> pdb=" O ASP B 767 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N THR B 783 " --> pdb=" O ILE B 779 " (cutoff:3.500A) Processing helix chain 'B' and resid 799 through 811 removed outlier: 3.923A pdb=" N LEU B 804 " --> pdb=" O LEU B 801 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU B 805 " --> pdb=" O PHE B 802 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ARG B 809 " --> pdb=" O ARG B 806 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N MET B 810 " --> pdb=" O GLY B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 856 Proline residue: B 819 - end of helix removed outlier: 3.835A pdb=" N ASP B 855 " --> pdb=" O GLY B 851 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N ARG B 856 " --> pdb=" O LYS B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 861 through 888 removed outlier: 4.108A pdb=" N LYS B 880 " --> pdb=" O LEU B 876 " (cutoff:3.500A) Processing helix chain 'B' and resid 890 through 919 removed outlier: 3.655A pdb=" N VAL B 894 " --> pdb=" O PRO B 890 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER B 895 " --> pdb=" O GLY B 891 " (cutoff:3.500A) Processing helix chain 'B' and resid 924 through 942 Processing helix chain 'A' and resid 76 through 94 removed outlier: 3.813A pdb=" N VAL A 79 " --> pdb=" O LYS A 76 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE A 80 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE A 81 " --> pdb=" O ILE A 78 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER A 82 " --> pdb=" O VAL A 79 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N SER A 84 " --> pdb=" O ILE A 81 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE A 90 " --> pdb=" O PHE A 87 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG A 92 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER A 93 " --> pdb=" O ILE A 90 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A 94 " --> pdb=" O SER A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 119 removed outlier: 3.501A pdb=" N VAL A 115 " --> pdb=" O ALA A 111 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASN A 119 " --> pdb=" O VAL A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 153 removed outlier: 4.509A pdb=" N LEU A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) Proline residue: A 144 - end of helix removed outlier: 3.725A pdb=" N SER A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 160 Processing helix chain 'A' and resid 163 through 188 removed outlier: 3.634A pdb=" N ILE A 168 " --> pdb=" O SER A 164 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N PHE A 172 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLY A 173 " --> pdb=" O LEU A 169 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA A 185 " --> pdb=" O THR A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 204 Processing helix chain 'A' and resid 211 through 217 Processing helix chain 'A' and resid 224 through 249 removed outlier: 3.960A pdb=" N GLU A 231 " --> pdb=" O GLY A 227 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU A 236 " --> pdb=" O GLY A 232 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE A 242 " --> pdb=" O ASP A 238 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A 243 " --> pdb=" O GLY A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 272 Processing helix chain 'A' and resid 274 through 290 Processing helix chain 'A' and resid 297 through 316 removed outlier: 3.542A pdb=" N TYR A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 336 Processing helix chain 'A' and resid 345 through 374 removed outlier: 3.853A pdb=" N THR A 373 " --> pdb=" O GLY A 369 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLN A 374 " --> pdb=" O VAL A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 412 removed outlier: 4.073A pdb=" N ILE A 389 " --> pdb=" O TRP A 385 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE A 390 " --> pdb=" O PHE A 386 " (cutoff:3.500A) Proline residue: A 408 - end of helix Processing helix chain 'A' and resid 419 through 427 removed outlier: 3.915A pdb=" N VAL A 423 " --> pdb=" O TRP A 419 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE A 424 " --> pdb=" O ARG A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 445 Processing helix chain 'A' and resid 454 through 481 removed outlier: 3.958A pdb=" N ALA A 471 " --> pdb=" O LEU A 467 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N THR A 472 " --> pdb=" O VAL A 468 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N GLN A 475 " --> pdb=" O ALA A 471 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N THR A 476 " --> pdb=" O THR A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 513 Processing helix chain 'A' and resid 524 through 529 Processing helix chain 'A' and resid 578 through 600 removed outlier: 3.967A pdb=" N LYS A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N SER A 593 " --> pdb=" O ALA A 589 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N TYR A 594 " --> pdb=" O GLU A 590 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N TRP A 595 " --> pdb=" O LYS A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 620 removed outlier: 3.561A pdb=" N HIS A 614 " --> pdb=" O LEU A 610 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA A 618 " --> pdb=" O HIS A 614 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA A 619 " --> pdb=" O ALA A 615 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP A 620 " --> pdb=" O GLU A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 638 Processing helix chain 'A' and resid 643 through 653 Processing helix chain 'A' and resid 815 through 857 Proline residue: A 819 - end of helix removed outlier: 3.816A pdb=" N ASN A 831 " --> pdb=" O LYS A 828 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY A 851 " --> pdb=" O GLU A 848 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ILE A 854 " --> pdb=" O GLY A 851 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ASP A 855 " --> pdb=" O LYS A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 888 removed outlier: 3.919A pdb=" N GLU A 866 " --> pdb=" O LYS A 862 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLN A 877 " --> pdb=" O THR A 873 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL A 878 " --> pdb=" O GLY A 874 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY A 883 " --> pdb=" O VAL A 879 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU A 888 " --> pdb=" O LEU A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 919 removed outlier: 3.673A pdb=" N VAL A 894 " --> pdb=" O PRO A 890 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG A 903 " --> pdb=" O ARG A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 942 788 hydrogen bonds defined for protein. 2205 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.23 Time building geometry restraints manager: 5.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1869 1.31 - 1.44: 2905 1.44 - 1.57: 6887 1.57 - 1.69: 4 1.69 - 1.82: 112 Bond restraints: 11777 Sorted by residual: bond pdb=" C11 CPL A1401 " pdb=" O3 CPL A1401 " ideal model delta sigma weight residual 1.327 1.415 -0.088 2.00e-02 2.50e+03 1.95e+01 bond pdb=" C11 CPL B1401 " pdb=" O3 CPL B1401 " ideal model delta sigma weight residual 1.327 1.415 -0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" C31 CPL A1401 " pdb=" O2 CPL A1401 " ideal model delta sigma weight residual 1.332 1.416 -0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" C31 CPL B1401 " pdb=" O2 CPL B1401 " ideal model delta sigma weight residual 1.332 1.413 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" C43 CPL A1401 " pdb=" C44 CPL A1401 " ideal model delta sigma weight residual 1.496 1.548 -0.052 2.00e-02 2.50e+03 6.78e+00 ... (remaining 11772 not shown) Histogram of bond angle deviations from ideal: 97.99 - 109.05: 594 109.05 - 120.11: 10455 120.11 - 131.17: 4894 131.17 - 142.23: 45 142.23 - 153.29: 2 Bond angle restraints: 15990 Sorted by residual: angle pdb=" C39 CPL A1401 " pdb=" C40 CPL A1401 " pdb=" C41 CPL A1401 " ideal model delta sigma weight residual 127.51 153.29 -25.78 3.00e+00 1.11e-01 7.39e+01 angle pdb=" C39 CPL B1401 " pdb=" C40 CPL B1401 " pdb=" C41 CPL B1401 " ideal model delta sigma weight residual 127.51 152.55 -25.04 3.00e+00 1.11e-01 6.96e+01 angle pdb=" O3P CPL A1401 " pdb=" P CPL A1401 " pdb=" O4P CPL A1401 " ideal model delta sigma weight residual 93.29 109.75 -16.46 3.00e+00 1.11e-01 3.01e+01 angle pdb=" O3P CPL B1401 " pdb=" P CPL B1401 " pdb=" O4P CPL B1401 " ideal model delta sigma weight residual 93.29 109.69 -16.40 3.00e+00 1.11e-01 2.99e+01 angle pdb=" C38 CPL B1401 " pdb=" C39 CPL B1401 " pdb=" C40 CPL B1401 " ideal model delta sigma weight residual 127.82 111.48 16.34 3.00e+00 1.11e-01 2.97e+01 ... (remaining 15985 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.69: 6805 35.69 - 71.38: 215 71.38 - 107.07: 23 107.07 - 142.75: 2 142.75 - 178.44: 3 Dihedral angle restraints: 7048 sinusoidal: 2638 harmonic: 4410 Sorted by residual: dihedral pdb=" O2 CPL B1401 " pdb=" C1 CPL B1401 " pdb=" C2 CPL B1401 " pdb=" O3P CPL B1401 " ideal model delta sinusoidal sigma weight residual 309.18 130.74 178.44 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C3 CPL B1401 " pdb=" C1 CPL B1401 " pdb=" C2 CPL B1401 " pdb=" O3P CPL B1401 " ideal model delta sinusoidal sigma weight residual 72.09 -109.78 -178.13 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C3 CPL A1401 " pdb=" C1 CPL A1401 " pdb=" C2 CPL A1401 " pdb=" O3P CPL A1401 " ideal model delta sinusoidal sigma weight residual 72.09 -72.57 144.66 1 3.00e+01 1.11e-03 1.94e+01 ... (remaining 7045 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1522 0.048 - 0.095: 360 0.095 - 0.143: 53 0.143 - 0.191: 0 0.191 - 0.238: 3 Chirality restraints: 1938 Sorted by residual: chirality pdb=" C2 CPL A1401 " pdb=" C1 CPL A1401 " pdb=" C3 CPL A1401 " pdb=" O2 CPL A1401 " both_signs ideal model delta sigma weight residual False -2.32 -2.55 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" C2 CPL B1401 " pdb=" C1 CPL B1401 " pdb=" C3 CPL B1401 " pdb=" O2 CPL B1401 " both_signs ideal model delta sigma weight residual False -2.32 -2.54 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CA GLU A 911 " pdb=" N GLU A 911 " pdb=" C GLU A 911 " pdb=" CB GLU A 911 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 1935 not shown) Planarity restraints: 1985 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 641 " 0.041 5.00e-02 4.00e+02 6.21e-02 6.18e+00 pdb=" N PRO A 642 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 642 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 642 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 352 " -0.018 2.00e-02 2.50e+03 1.82e-02 5.81e+00 pdb=" CG PHE A 352 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE A 352 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 352 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE A 352 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE A 352 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 352 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 643 " -0.012 2.00e-02 2.50e+03 1.22e-02 3.71e+00 pdb=" CG TRP A 643 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP A 643 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP A 643 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 643 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 643 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 643 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 643 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 643 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 643 " 0.000 2.00e-02 2.50e+03 ... (remaining 1982 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 271 2.70 - 3.25: 12735 3.25 - 3.80: 19245 3.80 - 4.35: 22263 4.35 - 4.90: 36423 Nonbonded interactions: 90937 Sorted by model distance: nonbonded pdb=" O ILE B 81 " pdb=" OG SER B 84 " model vdw 2.149 2.440 nonbonded pdb=" O GLY B 369 " pdb=" OG1 THR B 373 " model vdw 2.185 2.440 nonbonded pdb=" O MET B 133 " pdb=" ND2 ASN B 444 " model vdw 2.212 2.520 nonbonded pdb=" OG SER A 593 " pdb=" NE2 GLN A 597 " model vdw 2.246 2.520 nonbonded pdb=" N GLU B 344 " pdb=" OE1 GLU B 344 " model vdw 2.249 2.520 ... (remaining 90932 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 1.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.170 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 35.120 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 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 : 0.004 0.088 11777 Z= 0.248 Angle : 0.854 25.785 15990 Z= 0.384 Chirality : 0.040 0.238 1938 Planarity : 0.004 0.062 1985 Dihedral : 18.411 178.443 4186 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.09 % Allowed : 35.19 % Favored : 64.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.23), residues: 1510 helix: 1.79 (0.16), residues: 1144 sheet: None (None), residues: 0 loop : -0.62 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 643 HIS 0.004 0.001 HIS A 502 PHE 0.042 0.001 PHE A 352 TYR 0.010 0.001 TYR B 387 ARG 0.005 0.000 ARG A 856 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 129 time to evaluate : 1.280 Fit side-chains REVERT: B 200 MET cc_start: 0.8008 (ttt) cc_final: 0.7783 (ttm) REVERT: B 231 GLU cc_start: 0.8965 (mm-30) cc_final: 0.8656 (mm-30) outliers start: 1 outliers final: 0 residues processed: 130 average time/residue: 0.2291 time to fit residues: 43.9170 Evaluate side-chains 126 residues out of total 1295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 127 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 63 optimal weight: 40.0000 chunk 39 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 61 optimal weight: 20.0000 chunk 118 optimal weight: 3.9990 chunk 45 optimal weight: 8.9990 chunk 71 optimal weight: 4.9990 chunk 88 optimal weight: 0.0980 chunk 137 optimal weight: 7.9990 overall best weight: 2.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 600 HIS ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.0832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 11777 Z= 0.296 Angle : 0.623 7.385 15990 Z= 0.319 Chirality : 0.039 0.154 1938 Planarity : 0.004 0.062 1985 Dihedral : 10.883 170.794 1672 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.62 % Allowed : 31.85 % Favored : 63.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.22), residues: 1510 helix: 1.77 (0.15), residues: 1148 sheet: None (None), residues: 0 loop : -0.69 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 643 HIS 0.003 0.001 HIS A 914 PHE 0.017 0.001 PHE B 159 TYR 0.010 0.001 TYR A 191 ARG 0.005 0.000 ARG A 856 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 121 time to evaluate : 1.628 Fit side-chains REVERT: B 133 MET cc_start: 0.7381 (OUTLIER) cc_final: 0.6999 (mmt) REVERT: B 401 MET cc_start: 0.8832 (ttt) cc_final: 0.8454 (tmm) REVERT: B 578 MET cc_start: 0.8936 (ptp) cc_final: 0.8699 (ptt) REVERT: A 113 LEU cc_start: 0.9409 (tp) cc_final: 0.9206 (tt) REVERT: A 154 MET cc_start: 0.9069 (tpp) cc_final: 0.8793 (tpt) REVERT: A 199 MET cc_start: 0.8298 (tpp) cc_final: 0.8037 (mpp) REVERT: A 587 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.8882 (pp) outliers start: 54 outliers final: 28 residues processed: 166 average time/residue: 0.2234 time to fit residues: 56.9074 Evaluate side-chains 151 residues out of total 1295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 121 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 630 ASP Chi-restraints excluded: chain B residue 855 ASP Chi-restraints excluded: chain B residue 871 SER Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 635 TRP Chi-restraints excluded: chain A residue 869 HIS Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 936 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 76 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 37 optimal weight: 10.0000 chunk 137 optimal weight: 9.9990 chunk 148 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 136 optimal weight: 0.7980 chunk 46 optimal weight: 10.0000 chunk 110 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.0793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11777 Z= 0.172 Angle : 0.570 10.277 15990 Z= 0.281 Chirality : 0.038 0.142 1938 Planarity : 0.004 0.061 1985 Dihedral : 10.610 170.268 1672 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 4.54 % Allowed : 30.74 % Favored : 64.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.22), residues: 1510 helix: 1.95 (0.16), residues: 1147 sheet: None (None), residues: 0 loop : -0.70 (0.34), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 643 HIS 0.002 0.000 HIS B 157 PHE 0.013 0.001 PHE B 195 TYR 0.010 0.001 TYR A 594 ARG 0.003 0.000 ARG B 605 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 130 time to evaluate : 1.419 Fit side-chains REVERT: B 214 VAL cc_start: 0.9358 (OUTLIER) cc_final: 0.9066 (t) REVERT: B 231 GLU cc_start: 0.9045 (mm-30) cc_final: 0.8646 (mm-30) REVERT: B 337 GLU cc_start: 0.8331 (mp0) cc_final: 0.8097 (mp0) REVERT: B 367 MET cc_start: 0.7932 (mtm) cc_final: 0.7685 (mtm) REVERT: B 401 MET cc_start: 0.8816 (ttt) cc_final: 0.8398 (tmm) REVERT: B 418 THR cc_start: 0.8100 (OUTLIER) cc_final: 0.7647 (p) REVERT: B 579 MET cc_start: 0.7885 (mmp) cc_final: 0.7537 (mmm) REVERT: B 586 MET cc_start: 0.8962 (mmm) cc_final: 0.8685 (mmm) REVERT: B 590 GLU cc_start: 0.8978 (OUTLIER) cc_final: 0.8681 (mp0) REVERT: A 154 MET cc_start: 0.8996 (tpp) cc_final: 0.8612 (tpt) REVERT: A 199 MET cc_start: 0.8368 (tpp) cc_final: 0.7760 (mpp) outliers start: 53 outliers final: 34 residues processed: 172 average time/residue: 0.2066 time to fit residues: 54.2791 Evaluate side-chains 157 residues out of total 1295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 120 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 214 VAL Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 289 PHE Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 590 GLU Chi-restraints excluded: chain B residue 630 ASP Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 635 TRP Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 869 HIS Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 932 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 135 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 65 optimal weight: 8.9990 chunk 92 optimal weight: 0.5980 chunk 137 optimal weight: 7.9990 chunk 145 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 130 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.0985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11777 Z= 0.215 Angle : 0.590 8.880 15990 Z= 0.291 Chirality : 0.038 0.128 1938 Planarity : 0.004 0.061 1985 Dihedral : 10.433 168.559 1672 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 6.08 % Allowed : 29.88 % Favored : 64.04 % 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: 1.97 (0.22), residues: 1510 helix: 1.93 (0.16), residues: 1150 sheet: None (None), residues: 0 loop : -0.72 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 643 HIS 0.002 0.000 HIS B 157 PHE 0.019 0.001 PHE B 159 TYR 0.009 0.001 TYR B 312 ARG 0.003 0.000 ARG B 605 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 125 time to evaluate : 1.138 Fit side-chains revert: symmetry clash REVERT: B 337 GLU cc_start: 0.8409 (mp0) cc_final: 0.8037 (mp0) REVERT: B 401 MET cc_start: 0.8822 (ttt) cc_final: 0.8425 (tmm) REVERT: B 418 THR cc_start: 0.8024 (OUTLIER) cc_final: 0.7541 (p) REVERT: B 579 MET cc_start: 0.7886 (mmp) cc_final: 0.7378 (mmp) REVERT: B 586 MET cc_start: 0.9021 (mmm) cc_final: 0.8721 (mmm) REVERT: B 590 GLU cc_start: 0.8974 (OUTLIER) cc_final: 0.8686 (mp0) REVERT: B 632 LYS cc_start: 0.7650 (OUTLIER) cc_final: 0.7281 (ptpt) outliers start: 71 outliers final: 45 residues processed: 185 average time/residue: 0.2092 time to fit residues: 58.4360 Evaluate side-chains 169 residues out of total 1295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 121 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 289 PHE Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 590 GLU Chi-restraints excluded: chain B residue 630 ASP Chi-restraints excluded: chain B residue 632 LYS Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 270 GLN Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 635 TRP Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 869 HIS Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 932 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 121 optimal weight: 2.9990 chunk 82 optimal weight: 20.0000 chunk 2 optimal weight: 0.5980 chunk 108 optimal weight: 4.9990 chunk 60 optimal weight: 40.0000 chunk 124 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 chunk 131 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11777 Z= 0.233 Angle : 0.595 9.319 15990 Z= 0.295 Chirality : 0.038 0.135 1938 Planarity : 0.004 0.061 1985 Dihedral : 10.410 167.855 1672 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 5.99 % Allowed : 30.31 % Favored : 63.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.22), residues: 1510 helix: 1.93 (0.16), residues: 1150 sheet: None (None), residues: 0 loop : -0.77 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 643 HIS 0.002 0.001 HIS B 157 PHE 0.011 0.001 PHE B 80 TYR 0.008 0.001 TYR B 312 ARG 0.003 0.000 ARG B 605 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 128 time to evaluate : 1.400 Fit side-chains revert: symmetry clash REVERT: B 337 GLU cc_start: 0.8469 (mp0) cc_final: 0.8050 (mp0) REVERT: B 401 MET cc_start: 0.8843 (ttt) cc_final: 0.8415 (tmm) REVERT: B 418 THR cc_start: 0.7980 (OUTLIER) cc_final: 0.7486 (p) REVERT: B 579 MET cc_start: 0.7961 (mmp) cc_final: 0.7558 (mmp) REVERT: B 586 MET cc_start: 0.9013 (mmm) cc_final: 0.8713 (mmm) REVERT: B 590 GLU cc_start: 0.8986 (OUTLIER) cc_final: 0.8678 (mp0) REVERT: B 614 HIS cc_start: 0.8925 (OUTLIER) cc_final: 0.8715 (t-90) REVERT: B 632 LYS cc_start: 0.7798 (OUTLIER) cc_final: 0.7385 (ptpt) REVERT: B 857 MET cc_start: 0.8899 (mmp) cc_final: 0.8643 (mmp) REVERT: A 481 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8852 (mm) outliers start: 70 outliers final: 48 residues processed: 187 average time/residue: 0.2026 time to fit residues: 57.4960 Evaluate side-chains 176 residues out of total 1295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 123 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 289 PHE Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 590 GLU Chi-restraints excluded: chain B residue 614 HIS Chi-restraints excluded: chain B residue 630 ASP Chi-restraints excluded: chain B residue 632 LYS Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 270 GLN Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 635 TRP Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 869 HIS Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 936 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 49 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 85 optimal weight: 6.9990 chunk 36 optimal weight: 7.9990 chunk 146 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11777 Z= 0.246 Angle : 0.622 11.821 15990 Z= 0.308 Chirality : 0.039 0.167 1938 Planarity : 0.004 0.062 1985 Dihedral : 10.352 167.543 1672 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 5.82 % Allowed : 30.91 % Favored : 63.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.22), residues: 1510 helix: 1.92 (0.16), residues: 1148 sheet: None (None), residues: 0 loop : -0.70 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 643 HIS 0.003 0.001 HIS B 157 PHE 0.023 0.001 PHE B 159 TYR 0.008 0.001 TYR B 312 ARG 0.003 0.000 ARG B 605 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 126 time to evaluate : 1.634 Fit side-chains revert: symmetry clash REVERT: B 231 GLU cc_start: 0.8985 (mm-30) cc_final: 0.8627 (mm-30) REVERT: B 337 GLU cc_start: 0.8499 (mp0) cc_final: 0.8063 (mp0) REVERT: B 344 GLU cc_start: 0.8394 (pm20) cc_final: 0.8091 (pm20) REVERT: B 401 MET cc_start: 0.8861 (ttt) cc_final: 0.8427 (tmm) REVERT: B 418 THR cc_start: 0.8023 (OUTLIER) cc_final: 0.7519 (p) REVERT: B 579 MET cc_start: 0.7909 (mmp) cc_final: 0.7496 (mmp) REVERT: B 586 MET cc_start: 0.9003 (mmm) cc_final: 0.8700 (mmm) REVERT: B 590 GLU cc_start: 0.8980 (OUTLIER) cc_final: 0.8661 (mp0) REVERT: B 632 LYS cc_start: 0.7781 (OUTLIER) cc_final: 0.7352 (ptpt) REVERT: B 857 MET cc_start: 0.8969 (mmp) cc_final: 0.8255 (mmm) REVERT: A 481 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8855 (mm) REVERT: A 578 MET cc_start: 0.7677 (pmm) cc_final: 0.7464 (pmm) outliers start: 68 outliers final: 55 residues processed: 184 average time/residue: 0.2226 time to fit residues: 61.9225 Evaluate side-chains 181 residues out of total 1295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 122 time to evaluate : 1.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 289 PHE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 590 GLU Chi-restraints excluded: chain B residue 630 ASP Chi-restraints excluded: chain B residue 632 LYS Chi-restraints excluded: chain B residue 885 LEU Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 488 ILE Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 635 TRP Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 869 HIS Chi-restraints excluded: chain A residue 882 LEU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 936 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 140 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 106 optimal weight: 0.7980 chunk 82 optimal weight: 0.0970 chunk 122 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 145 optimal weight: 0.5980 chunk 91 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11777 Z= 0.152 Angle : 0.593 11.050 15990 Z= 0.288 Chirality : 0.038 0.148 1938 Planarity : 0.004 0.060 1985 Dihedral : 10.191 166.291 1672 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 4.45 % Allowed : 32.71 % Favored : 62.84 % 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: 2.17 (0.23), residues: 1510 helix: 2.08 (0.16), residues: 1143 sheet: None (None), residues: 0 loop : -0.61 (0.34), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 643 HIS 0.003 0.000 HIS B 614 PHE 0.011 0.001 PHE A 172 TYR 0.012 0.001 TYR A 594 ARG 0.004 0.000 ARG B 605 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 136 time to evaluate : 1.523 Fit side-chains REVERT: B 231 GLU cc_start: 0.8954 (mm-30) cc_final: 0.8570 (mm-30) REVERT: B 337 GLU cc_start: 0.8393 (mp0) cc_final: 0.7961 (mp0) REVERT: B 364 ILE cc_start: 0.9155 (OUTLIER) cc_final: 0.8928 (mp) REVERT: B 367 MET cc_start: 0.7831 (mtm) cc_final: 0.7548 (mtm) REVERT: B 401 MET cc_start: 0.8868 (ttt) cc_final: 0.8345 (tmm) REVERT: B 579 MET cc_start: 0.7897 (mmp) cc_final: 0.7461 (mmp) REVERT: B 586 MET cc_start: 0.9031 (mmm) cc_final: 0.8703 (mmp) REVERT: B 590 GLU cc_start: 0.8977 (OUTLIER) cc_final: 0.8648 (mp0) REVERT: B 857 MET cc_start: 0.8916 (mmp) cc_final: 0.8196 (mmm) REVERT: B 938 MET cc_start: 0.9373 (ttm) cc_final: 0.9141 (ttm) REVERT: A 481 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8885 (mm) REVERT: A 587 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.9013 (pp) REVERT: A 588 LYS cc_start: 0.9488 (mmmt) cc_final: 0.9238 (mmmt) outliers start: 52 outliers final: 34 residues processed: 178 average time/residue: 0.2209 time to fit residues: 59.7352 Evaluate side-chains 161 residues out of total 1295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 123 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain B residue 289 PHE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 590 GLU Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 936 ILE Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 635 TRP Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 869 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 90 optimal weight: 0.9980 chunk 58 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 13 optimal weight: 0.0980 chunk 114 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 830 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11777 Z= 0.202 Angle : 0.643 11.153 15990 Z= 0.311 Chirality : 0.039 0.207 1938 Planarity : 0.004 0.062 1985 Dihedral : 10.163 165.943 1672 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 4.37 % Allowed : 33.48 % Favored : 62.16 % 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: 2.06 (0.23), residues: 1510 helix: 1.96 (0.16), residues: 1154 sheet: None (None), residues: 0 loop : -0.59 (0.35), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 643 HIS 0.008 0.001 HIS B 614 PHE 0.023 0.001 PHE B 159 TYR 0.009 0.001 TYR B 312 ARG 0.003 0.000 ARG B 605 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 123 time to evaluate : 1.454 Fit side-chains revert: symmetry clash REVERT: B 337 GLU cc_start: 0.8490 (mp0) cc_final: 0.8076 (mp0) REVERT: B 401 MET cc_start: 0.8915 (ttt) cc_final: 0.8424 (tmm) REVERT: B 579 MET cc_start: 0.7939 (mmp) cc_final: 0.7500 (mmp) REVERT: B 586 MET cc_start: 0.9002 (mmm) cc_final: 0.8754 (mmm) REVERT: B 590 GLU cc_start: 0.8940 (OUTLIER) cc_final: 0.8620 (mp0) REVERT: B 857 MET cc_start: 0.8958 (mmp) cc_final: 0.8392 (mmm) REVERT: A 133 MET cc_start: 0.8747 (tpp) cc_final: 0.8207 (tpt) REVERT: A 481 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8907 (mm) REVERT: A 578 MET cc_start: 0.7598 (pmm) cc_final: 0.7369 (pmm) REVERT: A 587 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8838 (pp) REVERT: A 911 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.7989 (pm20) outliers start: 51 outliers final: 39 residues processed: 163 average time/residue: 0.2106 time to fit residues: 51.6014 Evaluate side-chains 161 residues out of total 1295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 118 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 289 PHE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 590 GLU Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 936 ILE Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 635 TRP Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 869 HIS Chi-restraints excluded: chain A residue 911 GLU Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 932 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 139 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 135 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 59 optimal weight: 50.0000 chunk 106 optimal weight: 0.9990 chunk 41 optimal weight: 0.0470 chunk 122 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 143 optimal weight: 6.9990 overall best weight: 1.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11777 Z= 0.200 Angle : 0.645 11.873 15990 Z= 0.312 Chirality : 0.039 0.206 1938 Planarity : 0.004 0.061 1985 Dihedral : 10.199 165.414 1672 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.20 % Allowed : 33.65 % Favored : 62.16 % 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: 2.03 (0.22), residues: 1510 helix: 1.97 (0.16), residues: 1148 sheet: None (None), residues: 0 loop : -0.67 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 635 HIS 0.005 0.000 HIS B 614 PHE 0.012 0.001 PHE A 386 TYR 0.008 0.001 TYR B 312 ARG 0.007 0.000 ARG A 585 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 125 time to evaluate : 1.419 Fit side-chains revert: symmetry clash REVERT: B 200 MET cc_start: 0.8207 (ttt) cc_final: 0.7999 (ttm) REVERT: B 337 GLU cc_start: 0.8504 (mp0) cc_final: 0.8090 (mp0) REVERT: B 367 MET cc_start: 0.7943 (mtm) cc_final: 0.7740 (mtm) REVERT: B 401 MET cc_start: 0.8913 (ttt) cc_final: 0.8446 (tmm) REVERT: B 579 MET cc_start: 0.7990 (mmp) cc_final: 0.7552 (mmp) REVERT: B 586 MET cc_start: 0.9029 (mmm) cc_final: 0.8783 (mmm) REVERT: B 590 GLU cc_start: 0.8954 (OUTLIER) cc_final: 0.8632 (mp0) REVERT: B 857 MET cc_start: 0.8987 (mmp) cc_final: 0.8406 (mmm) REVERT: A 133 MET cc_start: 0.8688 (tpp) cc_final: 0.8212 (tpt) REVERT: A 481 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8894 (mm) REVERT: A 586 MET cc_start: 0.9507 (tmm) cc_final: 0.9307 (ptt) outliers start: 49 outliers final: 40 residues processed: 164 average time/residue: 0.2118 time to fit residues: 52.1754 Evaluate side-chains 162 residues out of total 1295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 120 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 289 PHE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 590 GLU Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 936 ILE Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 635 TRP Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 869 HIS Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 932 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 87 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 150 optimal weight: 6.9990 chunk 138 optimal weight: 0.0270 chunk 119 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 92 optimal weight: 0.1980 chunk 73 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11777 Z= 0.156 Angle : 0.659 12.488 15990 Z= 0.312 Chirality : 0.039 0.223 1938 Planarity : 0.004 0.058 1985 Dihedral : 10.101 164.333 1672 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.68 % Allowed : 34.59 % Favored : 61.73 % 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: 2.13 (0.23), residues: 1510 helix: 2.03 (0.16), residues: 1149 sheet: None (None), residues: 0 loop : -0.59 (0.34), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP A 643 HIS 0.004 0.000 HIS B 614 PHE 0.024 0.001 PHE B 159 TYR 0.009 0.001 TYR A 594 ARG 0.004 0.000 ARG B 605 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 132 time to evaluate : 1.469 Fit side-chains revert: symmetry clash REVERT: B 200 MET cc_start: 0.8125 (ttt) cc_final: 0.7923 (ttm) REVERT: B 231 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8603 (mm-30) REVERT: B 337 GLU cc_start: 0.8448 (mp0) cc_final: 0.8059 (mp0) REVERT: B 367 MET cc_start: 0.7869 (mtm) cc_final: 0.7655 (mtm) REVERT: B 401 MET cc_start: 0.8918 (ttt) cc_final: 0.8425 (tmm) REVERT: B 579 MET cc_start: 0.7959 (mmp) cc_final: 0.7509 (mmp) REVERT: B 586 MET cc_start: 0.9027 (mmm) cc_final: 0.8695 (mmp) REVERT: B 590 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8606 (mp0) REVERT: B 641 TYR cc_start: 0.6099 (m-80) cc_final: 0.5892 (m-80) REVERT: B 938 MET cc_start: 0.9390 (ttm) cc_final: 0.9148 (ttm) REVERT: A 133 MET cc_start: 0.8569 (tpp) cc_final: 0.8182 (tpt) REVERT: A 646 ARG cc_start: 0.9194 (OUTLIER) cc_final: 0.8912 (mmp-170) outliers start: 43 outliers final: 37 residues processed: 166 average time/residue: 0.2159 time to fit residues: 53.1292 Evaluate side-chains 166 residues out of total 1295 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 127 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 187 ASN Chi-restraints excluded: chain B residue 204 ILE Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 289 PHE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 430 LEU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 590 GLU Chi-restraints excluded: chain B residue 821 LEU Chi-restraints excluded: chain B residue 936 ILE Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 233 GLU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 577 ASP Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 626 ILE Chi-restraints excluded: chain A residue 635 TRP Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 646 ARG Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 869 HIS Chi-restraints excluded: chain A residue 916 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 36 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 17 optimal weight: 0.7980 chunk 33 optimal weight: 10.0000 chunk 119 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 105 optimal weight: 0.0970 chunk 6 optimal weight: 5.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.093656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.070822 restraints weight = 40362.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.072602 restraints weight = 22269.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.073741 restraints weight = 15473.155| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11777 Z= 0.170 Angle : 0.667 12.803 15990 Z= 0.319 Chirality : 0.039 0.250 1938 Planarity : 0.004 0.064 1985 Dihedral : 10.060 163.720 1672 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.17 % Allowed : 35.70 % Favored : 61.13 % 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: 2.12 (0.23), residues: 1510 helix: 2.02 (0.16), residues: 1149 sheet: None (None), residues: 0 loop : -0.56 (0.34), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP A 643 HIS 0.004 0.000 HIS B 614 PHE 0.051 0.001 PHE A 352 TYR 0.008 0.001 TYR B 312 ARG 0.004 0.000 ARG A 910 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2213.47 seconds wall clock time: 41 minutes 30.60 seconds (2490.60 seconds total)