Starting phenix.real_space_refine on Tue Apr 9 00:37:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd9_36077/04_2024/8jd9_36077_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd9_36077/04_2024/8jd9_36077.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd9_36077/04_2024/8jd9_36077.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd9_36077/04_2024/8jd9_36077.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd9_36077/04_2024/8jd9_36077_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd9_36077/04_2024/8jd9_36077_neut_updated.pdb" } resolution = 2.87 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= 0.002 sd= 0.103 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 9609 2.51 5 N 2388 2.21 5 O 2666 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 221": "OD1" <-> "OD2" Residue "A PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 485": "OD1" <-> "OD2" Residue "A ASP 524": "OD1" <-> "OD2" Residue "A GLU 549": "OE1" <-> "OE2" Residue "A GLU 613": "OE1" <-> "OE2" Residue "A GLU 771": "OE1" <-> "OE2" Residue "B PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 524": "OD1" <-> "OD2" Residue "B ASP 577": "OD1" <-> "OD2" Residue "B TYR 634": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 820": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 877": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 14725 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 935, 7318 Classifications: {'peptide': 935} Link IDs: {'PTRANS': 33, 'TRANS': 901} Chain breaks: 4 Chain: "B" Number of atoms: 7318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 935, 7318 Classifications: {'peptide': 935} Link IDs: {'PTRANS': 33, 'TRANS': 901} Chain breaks: 4 Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 89 Unusual residues: {'PC1': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Time building chain proxies: 8.32, per 1000 atoms: 0.57 Number of scatterers: 14725 At special positions: 0 Unit cell: (104.76, 105.84, 130.68, 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 2666 8.00 N 2388 7.00 C 9609 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.98 Conformation dependent library (CDL) restraints added in 3.0 seconds 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3484 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 73 helices and 8 sheets defined 62.8% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.95 Creating SS restraints... Processing helix chain 'A' and resid 33 through 53 removed outlier: 3.551A pdb=" N LEU A 53 " --> pdb=" O SER A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 77 Processing helix chain 'A' and resid 85 through 95 removed outlier: 3.975A pdb=" N GLU A 95 " --> pdb=" O ARG A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 115 removed outlier: 3.508A pdb=" N LEU A 102 " --> pdb=" O PRO A 98 " (cutoff:3.500A) Proline residue: A 107 - end of helix removed outlier: 4.696A pdb=" N GLU A 112 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N SER A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 151 removed outlier: 4.367A pdb=" N ARG A 124 " --> pdb=" O HIS A 120 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N CYS A 125 " --> pdb=" O GLN A 121 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N GLY A 127 " --> pdb=" O LYS A 123 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N GLN A 128 " --> pdb=" O ARG A 124 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET A 129 " --> pdb=" O CYS A 125 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU A 132 " --> pdb=" O GLN A 128 " (cutoff:3.500A) Proline residue: A 135 - end of helix Processing helix chain 'A' and resid 158 through 168 Processing helix chain 'A' and resid 173 through 182 Processing helix chain 'A' and resid 187 through 216 removed outlier: 3.739A pdb=" N VAL A 206 " --> pdb=" O GLY A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 253 removed outlier: 4.935A pdb=" N GLY A 238 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE A 239 " --> pdb=" O GLY A 235 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N PHE A 253 " --> pdb=" O ILE A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 277 removed outlier: 3.591A pdb=" N THR A 265 " --> pdb=" O GLU A 261 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE A 266 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR A 274 " --> pdb=" O TYR A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 298 Processing helix chain 'A' and resid 305 through 338 removed outlier: 4.235A pdb=" N LYS A 309 " --> pdb=" O GLY A 305 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N SER A 310 " --> pdb=" O ASP A 306 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY A 331 " --> pdb=" O PHE A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 376 removed outlier: 3.778A pdb=" N PHE A 353 " --> pdb=" O ASN A 349 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N PHE A 355 " --> pdb=" O TRP A 351 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU A 356 " --> pdb=" O ARG A 352 " (cutoff:3.500A) Proline residue: A 374 - end of helix Processing helix chain 'A' and resid 385 through 391 Processing helix chain 'A' and resid 399 through 410 Processing helix chain 'A' and resid 419 through 450 removed outlier: 4.471A pdb=" N GLY A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER A 442 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG A 449 " --> pdb=" O GLN A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 481 removed outlier: 5.138A pdb=" N MET A 471 " --> pdb=" O THR A 467 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU A 472 " --> pdb=" O LYS A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 499 removed outlier: 3.762A pdb=" N TYR A 499 " --> pdb=" O THR A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 503 No H-bonds generated for 'chain 'A' and resid 501 through 503' Processing helix chain 'A' and resid 530 through 548 Processing helix chain 'A' and resid 554 through 569 removed outlier: 3.726A pdb=" N ASP A 569 " --> pdb=" O ASP A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 582 No H-bonds generated for 'chain 'A' and resid 579 through 582' Processing helix chain 'A' and resid 589 through 595 removed outlier: 3.617A pdb=" N PHE A 593 " --> pdb=" O TYR A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 611 removed outlier: 4.174A pdb=" N TYR A 606 " --> pdb=" O LYS A 602 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE A 607 " --> pdb=" O LEU A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 637 Processing helix chain 'A' and resid 641 through 667 removed outlier: 4.026A pdb=" N GLU A 655 " --> pdb=" O GLU A 651 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N GLU A 656 " --> pdb=" O LYS A 652 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ALA A 657 " --> pdb=" O GLU A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 697 removed outlier: 4.513A pdb=" N ARG A 673 " --> pdb=" O PRO A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 722 Processing helix chain 'A' and resid 734 through 738 Processing helix chain 'A' and resid 751 through 753 No H-bonds generated for 'chain 'A' and resid 751 through 753' Processing helix chain 'A' and resid 811 through 816 Processing helix chain 'A' and resid 837 through 845 removed outlier: 4.030A pdb=" N SER A 845 " --> pdb=" O LEU A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 865 removed outlier: 4.197A pdb=" N PHE A 852 " --> pdb=" O THR A 848 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL A 860 " --> pdb=" O GLU A 856 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LYS A 863 " --> pdb=" O LEU A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 870 No H-bonds generated for 'chain 'A' and resid 867 through 870' Processing helix chain 'A' and resid 875 through 883 removed outlier: 3.717A pdb=" N ALA A 880 " --> pdb=" O GLN A 876 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU A 881 " --> pdb=" O GLU A 877 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL A 882 " --> pdb=" O LEU A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1016 No H-bonds generated for 'chain 'A' and resid 1013 through 1016' Processing helix chain 'A' and resid 1033 through 1042 removed outlier: 3.825A pdb=" N ILE A1041 " --> pdb=" O MET A1037 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE A1042 " --> pdb=" O GLN A1038 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 53 removed outlier: 3.550A pdb=" N LEU B 53 " --> pdb=" O SER B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 77 Processing helix chain 'B' and resid 85 through 95 removed outlier: 3.757A pdb=" N GLU B 95 " --> pdb=" O ARG B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 115 Proline residue: B 107 - end of helix removed outlier: 4.732A pdb=" N GLU B 112 " --> pdb=" O ALA B 108 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N SER B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 124 removed outlier: 4.616A pdb=" N ARG B 124 " --> pdb=" O HIS B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 151 removed outlier: 3.542A pdb=" N LEU B 132 " --> pdb=" O GLN B 128 " (cutoff:3.500A) Proline residue: B 135 - end of helix Processing helix chain 'B' and resid 158 through 169 Processing helix chain 'B' and resid 173 through 182 Processing helix chain 'B' and resid 187 through 216 removed outlier: 3.699A pdb=" N VAL B 206 " --> pdb=" O GLY B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 253 removed outlier: 3.586A pdb=" N GLY B 235 " --> pdb=" O LYS B 231 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLY B 238 " --> pdb=" O LEU B 234 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE B 239 " --> pdb=" O GLY B 235 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE B 253 " --> pdb=" O ILE B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 277 removed outlier: 3.581A pdb=" N THR B 265 " --> pdb=" O GLU B 261 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE B 266 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TYR B 274 " --> pdb=" O TYR B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 298 Processing helix chain 'B' and resid 305 through 338 removed outlier: 4.113A pdb=" N LYS B 309 " --> pdb=" O GLY B 305 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N SER B 310 " --> pdb=" O ASP B 306 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY B 331 " --> pdb=" O PHE B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 378 removed outlier: 3.784A pdb=" N PHE B 353 " --> pdb=" O ASN B 349 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N PHE B 355 " --> pdb=" O TRP B 351 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU B 356 " --> pdb=" O ARG B 352 " (cutoff:3.500A) Proline residue: B 374 - end of helix removed outlier: 5.197A pdb=" N ARG B 378 " --> pdb=" O PRO B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 391 Processing helix chain 'B' and resid 399 through 410 Processing helix chain 'B' and resid 419 through 450 removed outlier: 4.386A pdb=" N GLY B 441 " --> pdb=" O LEU B 437 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER B 442 " --> pdb=" O ILE B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 481 removed outlier: 5.123A pdb=" N MET B 471 " --> pdb=" O THR B 467 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU B 472 " --> pdb=" O LYS B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 499 removed outlier: 3.723A pdb=" N TYR B 499 " --> pdb=" O THR B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 503 No H-bonds generated for 'chain 'B' and resid 501 through 503' Processing helix chain 'B' and resid 530 through 548 Processing helix chain 'B' and resid 554 through 569 removed outlier: 3.640A pdb=" N ASP B 569 " --> pdb=" O ASP B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 595 removed outlier: 3.854A pdb=" N PHE B 593 " --> pdb=" O TYR B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 637 removed outlier: 3.596A pdb=" N THR B 605 " --> pdb=" O ARG B 601 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N TYR B 606 " --> pdb=" O LYS B 602 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE B 607 " --> pdb=" O LEU B 603 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N SER B 614 " --> pdb=" O GLU B 610 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ALA B 615 " --> pdb=" O ARG B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 667 removed outlier: 3.949A pdb=" N GLU B 655 " --> pdb=" O GLU B 651 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N GLU B 656 " --> pdb=" O LYS B 652 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ALA B 657 " --> pdb=" O GLU B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 697 removed outlier: 4.533A pdb=" N ARG B 673 " --> pdb=" O PRO B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 722 Processing helix chain 'B' and resid 734 through 738 Processing helix chain 'B' and resid 751 through 753 No H-bonds generated for 'chain 'B' and resid 751 through 753' Processing helix chain 'B' and resid 811 through 816 Processing helix chain 'B' and resid 837 through 845 removed outlier: 4.038A pdb=" N SER B 845 " --> pdb=" O LEU B 841 " (cutoff:3.500A) Processing helix chain 'B' and resid 847 through 865 removed outlier: 4.320A pdb=" N PHE B 852 " --> pdb=" O THR B 848 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL B 860 " --> pdb=" O GLU B 856 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LYS B 863 " --> pdb=" O LEU B 859 " (cutoff:3.500A) Processing helix chain 'B' and resid 867 through 870 No H-bonds generated for 'chain 'B' and resid 867 through 870' Processing helix chain 'B' and resid 875 through 883 removed outlier: 3.696A pdb=" N ALA B 880 " --> pdb=" O GLN B 876 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU B 881 " --> pdb=" O GLU B 877 " (cutoff:3.500A) Processing helix chain 'B' and resid 1013 through 1016 No H-bonds generated for 'chain 'B' and resid 1013 through 1016' Processing helix chain 'B' and resid 1033 through 1042 Processing sheet with id= A, first strand: chain 'A' and resid 807 through 809 removed outlier: 3.687A pdb=" N SER A 807 " --> pdb=" O ILE A 781 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU A 831 " --> pdb=" O PHE A 782 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 786 through 789 Processing sheet with id= C, first strand: chain 'A' and resid 890 through 892 removed outlier: 3.583A pdb=" N ALA A 967 " --> pdb=" O THR A 890 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG A 966 " --> pdb=" O GLU A 910 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU A 910 " --> pdb=" O ARG A 966 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ILE A 968 " --> pdb=" O LEU A 908 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N LEU A 908 " --> pdb=" O ILE A 968 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 897 through 899 Processing sheet with id= E, first strand: chain 'B' and resid 807 through 809 removed outlier: 3.662A pdb=" N SER B 807 " --> pdb=" O ILE B 781 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU B 831 " --> pdb=" O PHE B 782 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 786 through 789 Processing sheet with id= G, first strand: chain 'B' and resid 889 through 892 removed outlier: 3.673A pdb=" N ARG B 966 " --> pdb=" O GLU B 910 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU B 910 " --> pdb=" O ARG B 966 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ILE B 968 " --> pdb=" O LEU B 908 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N LEU B 908 " --> pdb=" O ILE B 968 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 913 through 915 819 hydrogen bonds defined for protein. 2322 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: 4.94 Time building geometry restraints manager: 6.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2492 1.33 - 1.45: 3754 1.45 - 1.57: 8679 1.57 - 1.69: 4 1.69 - 1.81: 102 Bond restraints: 15031 Sorted by residual: bond pdb=" CB PRO B 926 " pdb=" CG PRO B 926 " ideal model delta sigma weight residual 1.492 1.548 -0.056 5.00e-02 4.00e+02 1.25e+00 bond pdb=" CG LEU A 720 " pdb=" CD1 LEU A 720 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.25e+00 bond pdb=" CB PRO A 926 " pdb=" CG PRO A 926 " ideal model delta sigma weight residual 1.492 1.548 -0.056 5.00e-02 4.00e+02 1.24e+00 bond pdb=" CG LEU B 720 " pdb=" CD1 LEU B 720 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.14e+00 bond pdb=" N TRP B 279 " pdb=" CA TRP B 279 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.29e-02 6.01e+03 1.11e+00 ... (remaining 15026 not shown) Histogram of bond angle deviations from ideal: 99.62 - 106.50: 361 106.50 - 113.37: 8519 113.37 - 120.25: 5251 120.25 - 127.13: 6059 127.13 - 134.00: 165 Bond angle restraints: 20355 Sorted by residual: angle pdb=" C GLU B 278 " pdb=" N TRP B 279 " pdb=" CA TRP B 279 " ideal model delta sigma weight residual 121.54 131.71 -10.17 1.91e+00 2.74e-01 2.83e+01 angle pdb=" C GLU A 278 " pdb=" N TRP A 279 " pdb=" CA TRP A 279 " ideal model delta sigma weight residual 121.54 131.68 -10.14 1.91e+00 2.74e-01 2.82e+01 angle pdb=" CA PRO B 926 " pdb=" N PRO B 926 " pdb=" CD PRO B 926 " ideal model delta sigma weight residual 112.00 107.67 4.33 1.40e+00 5.10e-01 9.56e+00 angle pdb=" CA PRO A 926 " pdb=" N PRO A 926 " pdb=" CD PRO A 926 " ideal model delta sigma weight residual 112.00 107.76 4.24 1.40e+00 5.10e-01 9.17e+00 angle pdb=" N TRP B 279 " pdb=" CA TRP B 279 " pdb=" CB TRP B 279 " ideal model delta sigma weight residual 110.49 115.44 -4.95 1.69e+00 3.50e-01 8.59e+00 ... (remaining 20350 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.17: 8090 17.17 - 34.34: 718 34.34 - 51.51: 117 51.51 - 68.68: 28 68.68 - 85.85: 22 Dihedral angle restraints: 8975 sinusoidal: 3573 harmonic: 5402 Sorted by residual: dihedral pdb=" CA SER A 925 " pdb=" C SER A 925 " pdb=" N PRO A 926 " pdb=" CA PRO A 926 " ideal model delta harmonic sigma weight residual -180.00 -140.81 -39.19 0 5.00e+00 4.00e-02 6.14e+01 dihedral pdb=" CA SER B 925 " pdb=" C SER B 925 " pdb=" N PRO B 926 " pdb=" CA PRO B 926 " ideal model delta harmonic sigma weight residual 180.00 -140.97 -39.03 0 5.00e+00 4.00e-02 6.09e+01 dihedral pdb=" CA SER A 341 " pdb=" C SER A 341 " pdb=" N ASP A 342 " pdb=" CA ASP A 342 " ideal model delta harmonic sigma weight residual -180.00 -152.00 -28.00 0 5.00e+00 4.00e-02 3.14e+01 ... (remaining 8972 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1487 0.028 - 0.055: 578 0.055 - 0.083: 218 0.083 - 0.110: 80 0.110 - 0.137: 29 Chirality restraints: 2392 Sorted by residual: chirality pdb=" CA PRO A 926 " pdb=" N PRO A 926 " pdb=" C PRO A 926 " pdb=" CB PRO A 926 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.73e-01 chirality pdb=" CA VAL B 392 " pdb=" N VAL B 392 " pdb=" C VAL B 392 " pdb=" CB VAL B 392 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.44e-01 chirality pdb=" CA PRO B 926 " pdb=" N PRO B 926 " pdb=" C PRO B 926 " pdb=" CB PRO B 926 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.43e-01 ... (remaining 2389 not shown) Planarity restraints: 2494 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 925 " -0.090 5.00e-02 4.00e+02 1.36e-01 2.98e+01 pdb=" N PRO B 926 " 0.236 5.00e-02 4.00e+02 pdb=" CA PRO B 926 " -0.074 5.00e-02 4.00e+02 pdb=" CD PRO B 926 " -0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 925 " 0.089 5.00e-02 4.00e+02 1.35e-01 2.92e+01 pdb=" N PRO A 926 " -0.234 5.00e-02 4.00e+02 pdb=" CA PRO A 926 " 0.073 5.00e-02 4.00e+02 pdb=" CD PRO A 926 " 0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 582 " -0.029 5.00e-02 4.00e+02 4.42e-02 3.13e+00 pdb=" N PRO B 583 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO B 583 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 583 " -0.025 5.00e-02 4.00e+02 ... (remaining 2491 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 341 2.71 - 3.26: 15264 3.26 - 3.80: 24198 3.80 - 4.35: 31633 4.35 - 4.90: 53219 Nonbonded interactions: 124655 Sorted by model distance: nonbonded pdb=" O ARG A 551 " pdb=" NE2 GLN A 679 " model vdw 2.162 2.520 nonbonded pdb=" OD1 ASN A 795 " pdb=" OG SER A 798 " model vdw 2.189 2.440 nonbonded pdb=" OH TYR A 274 " pdb=" OD1 ASP B 35 " model vdw 2.196 2.440 nonbonded pdb=" OD1 ASP A 35 " pdb=" OH TYR B 274 " model vdw 2.201 2.440 nonbonded pdb=" OH TYR B 617 " pdb=" O VAL B 675 " model vdw 2.253 2.440 ... (remaining 124650 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 28 through 1047) selection = chain 'B' } 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: 0.890 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: 4.390 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 43.160 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.080 Set refine NCS operators: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 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 : 0.002 0.056 15031 Z= 0.158 Angle : 0.559 10.169 20355 Z= 0.285 Chirality : 0.037 0.137 2392 Planarity : 0.005 0.136 2494 Dihedral : 13.879 85.846 5491 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.24 % Favored : 94.43 % Rotamer: Outliers : 0.06 % Allowed : 0.25 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: 1.03 (0.20), residues: 1850 helix: 1.46 (0.15), residues: 1204 sheet: 2.36 (0.57), residues: 94 loop : -1.38 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 393 HIS 0.004 0.001 HIS A 626 PHE 0.012 0.001 PHE A 749 TYR 0.014 0.001 TYR B 590 ARG 0.009 0.000 ARG A 378 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 224 time to evaluate : 1.778 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 761 MET cc_start: 0.7584 (ttt) cc_final: 0.7097 (ttt) REVERT: B 670 GLN cc_start: 0.7519 (pm20) cc_final: 0.7278 (pm20) REVERT: B 761 MET cc_start: 0.7579 (ttt) cc_final: 0.7087 (ttt) outliers start: 1 outliers final: 0 residues processed: 225 average time/residue: 1.2694 time to fit residues: 314.9576 Evaluate side-chains 154 residues out of total 1618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 1.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 0.7980 chunk 140 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 145 optimal weight: 0.2980 chunk 56 optimal weight: 0.9990 chunk 88 optimal weight: 40.0000 chunk 108 optimal weight: 8.9990 chunk 168 optimal weight: 7.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN B 94 ASN B 349 ASN ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 694 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.0931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 15031 Z= 0.192 Angle : 0.572 10.687 20355 Z= 0.289 Chirality : 0.039 0.168 2392 Planarity : 0.006 0.134 2494 Dihedral : 6.695 74.377 2063 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.51 % Favored : 94.16 % Rotamer: Outliers : 1.55 % Allowed : 9.09 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: 1.02 (0.20), residues: 1850 helix: 1.37 (0.15), residues: 1212 sheet: 2.57 (0.54), residues: 94 loop : -1.25 (0.27), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 315 HIS 0.007 0.001 HIS A 626 PHE 0.015 0.001 PHE B 636 TYR 0.019 0.001 TYR B 812 ARG 0.005 0.000 ARG A 378 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 173 time to evaluate : 1.700 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 670 GLN cc_start: 0.7552 (pm20) cc_final: 0.7305 (pm20) REVERT: B 770 LYS cc_start: 0.7736 (mmmt) cc_final: 0.7534 (mmmt) outliers start: 25 outliers final: 11 residues processed: 185 average time/residue: 1.0629 time to fit residues: 223.3310 Evaluate side-chains 163 residues out of total 1618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 152 time to evaluate : 1.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 783 ASP Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 825 ILE Chi-restraints excluded: chain B residue 856 GLU Chi-restraints excluded: chain B residue 968 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 93 optimal weight: 0.8980 chunk 52 optimal weight: 0.0980 chunk 140 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 169 optimal weight: 0.0010 chunk 182 optimal weight: 30.0000 chunk 150 optimal weight: 2.9990 chunk 167 optimal weight: 7.9990 chunk 57 optimal weight: 0.5980 chunk 135 optimal weight: 2.9990 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 323 ASN ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 GLN B 94 ASN B 323 ASN B 349 ASN ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 15031 Z= 0.163 Angle : 0.544 10.577 20355 Z= 0.272 Chirality : 0.038 0.318 2392 Planarity : 0.005 0.133 2494 Dihedral : 6.407 59.457 2063 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.30 % Favored : 94.38 % Rotamer: Outliers : 1.92 % Allowed : 11.43 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: 1.12 (0.20), residues: 1850 helix: 1.42 (0.15), residues: 1214 sheet: 3.02 (0.58), residues: 82 loop : -1.14 (0.27), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 279 HIS 0.005 0.001 HIS A 626 PHE 0.018 0.001 PHE B 636 TYR 0.015 0.001 TYR A 812 ARG 0.005 0.000 ARG A 378 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 172 time to evaluate : 1.751 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 472 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.8001 (tt) REVERT: A 761 MET cc_start: 0.7578 (OUTLIER) cc_final: 0.7319 (tmm) REVERT: B 670 GLN cc_start: 0.7562 (pm20) cc_final: 0.7322 (pm20) REVERT: B 761 MET cc_start: 0.7609 (OUTLIER) cc_final: 0.7369 (tmm) REVERT: B 770 LYS cc_start: 0.7665 (mmmt) cc_final: 0.7429 (mmmt) outliers start: 31 outliers final: 15 residues processed: 186 average time/residue: 1.0826 time to fit residues: 226.5223 Evaluate side-chains 172 residues out of total 1618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 154 time to evaluate : 1.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 532 ARG Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain A residue 783 ASP Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain A residue 856 GLU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 349 ASN Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 761 MET Chi-restraints excluded: chain B residue 825 ILE Chi-restraints excluded: chain B residue 856 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 80 optimal weight: 7.9990 chunk 113 optimal weight: 1.9990 chunk 169 optimal weight: 8.9990 chunk 179 optimal weight: 0.0980 chunk 88 optimal weight: 2.9990 chunk 160 optimal weight: 4.9990 chunk 48 optimal weight: 0.4980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 570 GLN B 94 ASN ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 15031 Z= 0.215 Angle : 0.562 10.709 20355 Z= 0.281 Chirality : 0.039 0.279 2392 Planarity : 0.005 0.132 2494 Dihedral : 6.387 58.289 2063 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.35 % Favored : 94.32 % Rotamer: Outliers : 2.72 % Allowed : 12.42 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: 0.99 (0.20), residues: 1850 helix: 1.32 (0.15), residues: 1212 sheet: 3.06 (0.58), residues: 82 loop : -1.18 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 315 HIS 0.009 0.001 HIS A 626 PHE 0.018 0.001 PHE A 636 TYR 0.019 0.001 TYR B 812 ARG 0.003 0.000 ARG A 378 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 166 time to evaluate : 1.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 472 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8061 (tt) REVERT: A 562 GLN cc_start: 0.7323 (OUTLIER) cc_final: 0.7065 (pt0) REVERT: A 761 MET cc_start: 0.7600 (OUTLIER) cc_final: 0.7330 (tmm) REVERT: B 670 GLN cc_start: 0.7599 (pm20) cc_final: 0.7342 (pm20) REVERT: B 761 MET cc_start: 0.7578 (OUTLIER) cc_final: 0.7319 (tmm) outliers start: 44 outliers final: 19 residues processed: 185 average time/residue: 1.0074 time to fit residues: 210.0936 Evaluate side-chains 180 residues out of total 1618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 157 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 532 ARG Chi-restraints excluded: chain A residue 562 GLN Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain A residue 783 ASP Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain A residue 856 GLU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 666 SER Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 761 MET Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 825 ILE Chi-restraints excluded: chain B residue 856 GLU Chi-restraints excluded: chain B residue 882 VAL Chi-restraints excluded: chain B residue 968 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 149 optimal weight: 0.4980 chunk 102 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 133 optimal weight: 0.7980 chunk 74 optimal weight: 8.9990 chunk 153 optimal weight: 0.7980 chunk 124 optimal weight: 0.0060 chunk 0 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 161 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 480 GLN A 570 GLN B 94 ASN ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 570 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 15031 Z= 0.170 Angle : 0.544 13.221 20355 Z= 0.269 Chirality : 0.038 0.260 2392 Planarity : 0.005 0.132 2494 Dihedral : 6.290 59.903 2063 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.41 % Favored : 94.27 % Rotamer: Outliers : 2.60 % Allowed : 13.35 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: 1.14 (0.20), residues: 1850 helix: 1.45 (0.15), residues: 1202 sheet: 3.18 (0.58), residues: 82 loop : -1.13 (0.27), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 279 HIS 0.006 0.001 HIS B 626 PHE 0.019 0.001 PHE B 636 TYR 0.017 0.001 TYR A 812 ARG 0.007 0.000 ARG A 378 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 171 time to evaluate : 1.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 472 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8074 (tt) REVERT: A 562 GLN cc_start: 0.7265 (OUTLIER) cc_final: 0.7016 (pt0) REVERT: B 761 MET cc_start: 0.7541 (OUTLIER) cc_final: 0.7340 (tmm) outliers start: 42 outliers final: 26 residues processed: 193 average time/residue: 1.0589 time to fit residues: 231.4322 Evaluate side-chains 189 residues out of total 1618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 160 time to evaluate : 1.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 532 ARG Chi-restraints excluded: chain A residue 562 GLN Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 783 ASP Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain A residue 856 GLU Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 182 GLU Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 571 VAL Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 728 LYS Chi-restraints excluded: chain B residue 761 MET Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 825 ILE Chi-restraints excluded: chain B residue 856 GLU Chi-restraints excluded: chain B residue 881 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 60 optimal weight: 0.0870 chunk 161 optimal weight: 0.0470 chunk 35 optimal weight: 0.0970 chunk 105 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 179 optimal weight: 9.9990 chunk 149 optimal weight: 0.5980 chunk 83 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 overall best weight: 0.2854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 570 GLN B 94 ASN ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 570 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 15031 Z= 0.150 Angle : 0.529 11.751 20355 Z= 0.264 Chirality : 0.037 0.265 2392 Planarity : 0.005 0.131 2494 Dihedral : 6.034 58.526 2063 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.35 % Favored : 94.32 % Rotamer: Outliers : 2.35 % Allowed : 14.96 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: 1.34 (0.20), residues: 1850 helix: 1.60 (0.15), residues: 1200 sheet: 3.32 (0.59), residues: 82 loop : -1.03 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 279 HIS 0.005 0.001 HIS A 626 PHE 0.018 0.001 PHE B 636 TYR 0.016 0.001 TYR B 812 ARG 0.006 0.000 ARG A 378 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 177 time to evaluate : 1.753 Fit side-chains revert: symmetry clash REVERT: A 472 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8031 (tt) REVERT: A 562 GLN cc_start: 0.7243 (OUTLIER) cc_final: 0.6955 (pt0) REVERT: B 907 LEU cc_start: 0.8449 (tt) cc_final: 0.8237 (tt) outliers start: 38 outliers final: 17 residues processed: 199 average time/residue: 1.0412 time to fit residues: 234.0994 Evaluate side-chains 188 residues out of total 1618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 169 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 562 GLN Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 783 ASP Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain A residue 856 GLU Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 728 LYS Chi-restraints excluded: chain B residue 735 MET Chi-restraints excluded: chain B residue 825 ILE Chi-restraints excluded: chain B residue 856 GLU Chi-restraints excluded: chain B residue 881 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 173 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 102 optimal weight: 0.9990 chunk 131 optimal weight: 10.0000 chunk 101 optimal weight: 0.9980 chunk 151 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 179 optimal weight: 7.9990 chunk 112 optimal weight: 6.9990 chunk 109 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 562 GLN B 570 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 15031 Z= 0.203 Angle : 0.562 11.184 20355 Z= 0.280 Chirality : 0.039 0.291 2392 Planarity : 0.005 0.131 2494 Dihedral : 6.093 59.185 2063 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.08 % Favored : 94.59 % Rotamer: Outliers : 2.66 % Allowed : 15.76 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: 1.20 (0.20), residues: 1850 helix: 1.48 (0.15), residues: 1198 sheet: 3.30 (0.58), residues: 82 loop : -1.06 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 279 HIS 0.007 0.001 HIS A 626 PHE 0.012 0.001 PHE A 636 TYR 0.024 0.001 TYR A 606 ARG 0.007 0.000 ARG A 378 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 164 time to evaluate : 1.776 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 532 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.7926 (mtt90) REVERT: A 562 GLN cc_start: 0.7155 (OUTLIER) cc_final: 0.6874 (pt0) outliers start: 43 outliers final: 25 residues processed: 190 average time/residue: 1.0099 time to fit residues: 218.2530 Evaluate side-chains 182 residues out of total 1618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 155 time to evaluate : 1.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 532 ARG Chi-restraints excluded: chain A residue 562 GLN Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 783 ASP Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain A residue 856 GLU Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 571 VAL Chi-restraints excluded: chain B residue 728 LYS Chi-restraints excluded: chain B residue 735 MET Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 825 ILE Chi-restraints excluded: chain B residue 856 GLU Chi-restraints excluded: chain B residue 881 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 110 optimal weight: 1.9990 chunk 71 optimal weight: 0.0050 chunk 107 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 113 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 16 optimal weight: 0.6980 chunk 140 optimal weight: 2.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 570 GLN B 94 ASN ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 570 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 15031 Z= 0.165 Angle : 0.544 12.098 20355 Z= 0.270 Chirality : 0.038 0.309 2392 Planarity : 0.005 0.130 2494 Dihedral : 5.955 59.250 2063 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.35 % Favored : 94.32 % Rotamer: Outliers : 2.35 % Allowed : 16.13 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: 1.28 (0.20), residues: 1850 helix: 1.55 (0.15), residues: 1200 sheet: 3.32 (0.59), residues: 82 loop : -1.06 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 279 HIS 0.005 0.001 HIS B 626 PHE 0.015 0.001 PHE B 607 TYR 0.015 0.001 TYR A 812 ARG 0.008 0.000 ARG A 378 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 159 time to evaluate : 1.724 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 562 GLN cc_start: 0.7177 (OUTLIER) cc_final: 0.6823 (pt0) REVERT: B 789 LYS cc_start: 0.7169 (tptt) cc_final: 0.6911 (tptm) outliers start: 38 outliers final: 24 residues processed: 181 average time/residue: 1.0690 time to fit residues: 219.0358 Evaluate side-chains 181 residues out of total 1618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 156 time to evaluate : 1.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 532 ARG Chi-restraints excluded: chain A residue 562 GLN Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 783 ASP Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain A residue 856 GLU Chi-restraints excluded: chain A residue 968 ILE Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 728 LYS Chi-restraints excluded: chain B residue 735 MET Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 825 ILE Chi-restraints excluded: chain B residue 832 CYS Chi-restraints excluded: chain B residue 856 GLU Chi-restraints excluded: chain B residue 881 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 163 optimal weight: 40.0000 chunk 171 optimal weight: 5.9990 chunk 156 optimal weight: 0.6980 chunk 167 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 150 optimal weight: 0.6980 chunk 158 optimal weight: 0.9980 chunk 166 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 562 GLN B 570 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 15031 Z= 0.188 Angle : 0.567 13.055 20355 Z= 0.279 Chirality : 0.039 0.326 2392 Planarity : 0.005 0.130 2494 Dihedral : 5.969 59.874 2063 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.19 % Favored : 94.49 % Rotamer: Outliers : 2.60 % Allowed : 15.82 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: 1.20 (0.20), residues: 1850 helix: 1.46 (0.15), residues: 1204 sheet: 3.34 (0.59), residues: 82 loop : -1.03 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B 279 HIS 0.006 0.001 HIS A 626 PHE 0.011 0.001 PHE B 622 TYR 0.015 0.001 TYR A 812 ARG 0.007 0.000 ARG A 378 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 158 time to evaluate : 1.757 Fit side-chains revert: symmetry clash REVERT: A 562 GLN cc_start: 0.7111 (OUTLIER) cc_final: 0.6842 (tt0) REVERT: A 606 TYR cc_start: 0.7501 (t80) cc_final: 0.7289 (t80) REVERT: B 789 LYS cc_start: 0.7162 (tptt) cc_final: 0.6908 (tptm) outliers start: 42 outliers final: 29 residues processed: 183 average time/residue: 1.0638 time to fit residues: 220.2668 Evaluate side-chains 184 residues out of total 1618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 154 time to evaluate : 1.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 562 GLN Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 666 SER Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 783 ASP Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain A residue 856 GLU Chi-restraints excluded: chain A residue 861 LEU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 571 VAL Chi-restraints excluded: chain B residue 728 LYS Chi-restraints excluded: chain B residue 735 MET Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 825 ILE Chi-restraints excluded: chain B residue 832 CYS Chi-restraints excluded: chain B residue 856 GLU Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 881 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 109 optimal weight: 1.9990 chunk 176 optimal weight: 10.0000 chunk 107 optimal weight: 0.7980 chunk 83 optimal weight: 0.0980 chunk 122 optimal weight: 1.9990 chunk 185 optimal weight: 0.6980 chunk 170 optimal weight: 0.9980 chunk 147 optimal weight: 0.0970 chunk 15 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 562 GLN B 570 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 15031 Z= 0.167 Angle : 0.567 13.137 20355 Z= 0.278 Chirality : 0.038 0.325 2392 Planarity : 0.005 0.130 2494 Dihedral : 5.904 59.156 2063 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.41 % Favored : 94.27 % Rotamer: Outliers : 1.85 % Allowed : 16.69 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: 1.27 (0.20), residues: 1850 helix: 1.51 (0.15), residues: 1204 sheet: 3.38 (0.59), residues: 82 loop : -1.03 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP B 279 HIS 0.005 0.001 HIS B 626 PHE 0.017 0.001 PHE B 607 TYR 0.014 0.001 TYR B 590 ARG 0.007 0.000 ARG A 378 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 156 time to evaluate : 1.749 Fit side-chains revert: symmetry clash REVERT: A 562 GLN cc_start: 0.7129 (OUTLIER) cc_final: 0.6853 (tt0) REVERT: B 570 GLN cc_start: 0.6546 (mt0) cc_final: 0.6297 (pp30) REVERT: B 789 LYS cc_start: 0.7110 (tptt) cc_final: 0.6901 (tptm) outliers start: 30 outliers final: 23 residues processed: 171 average time/residue: 1.0444 time to fit residues: 202.2667 Evaluate side-chains 174 residues out of total 1618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 150 time to evaluate : 1.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 384 ASP Chi-restraints excluded: chain A residue 562 GLN Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 671 VAL Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain A residue 783 ASP Chi-restraints excluded: chain A residue 825 ILE Chi-restraints excluded: chain A residue 856 GLU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 260 ILE Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 571 VAL Chi-restraints excluded: chain B residue 728 LYS Chi-restraints excluded: chain B residue 735 MET Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 825 ILE Chi-restraints excluded: chain B residue 832 CYS Chi-restraints excluded: chain B residue 856 GLU Chi-restraints excluded: chain B residue 881 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 117 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 147 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 151 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN ** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 562 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.179429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.140322 restraints weight = 15792.249| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 1.57 r_work: 0.3515 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 15031 Z= 0.218 Angle : 0.594 12.840 20355 Z= 0.292 Chirality : 0.040 0.333 2392 Planarity : 0.005 0.130 2494 Dihedral : 6.037 58.833 2063 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.30 % Favored : 94.38 % Rotamer: Outliers : 2.04 % Allowed : 16.50 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % 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: 1.08 (0.20), residues: 1850 helix: 1.37 (0.15), residues: 1200 sheet: 3.12 (0.57), residues: 88 loop : -1.10 (0.27), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP B 279 HIS 0.007 0.001 HIS B 626 PHE 0.012 0.001 PHE B 622 TYR 0.020 0.001 TYR A 812 ARG 0.007 0.000 ARG A 378 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4652.04 seconds wall clock time: 87 minutes 3.96 seconds (5223.96 seconds total)