Starting phenix.real_space_refine on Thu Mar 21 18:01:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pzp_13735/03_2024/7pzp_13735.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pzp_13735/03_2024/7pzp_13735.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pzp_13735/03_2024/7pzp_13735.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pzp_13735/03_2024/7pzp_13735.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pzp_13735/03_2024/7pzp_13735.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pzp_13735/03_2024/7pzp_13735.pdb" } resolution = 3.5 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= 0.001 sd= 0.053 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 15333 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 98 5.16 5 C 9912 2.51 5 N 2834 2.21 5 O 2758 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 1146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 601": "NH1" <-> "NH2" Residue "B PHE 1146": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15602 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7803 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 990, 7798 Classifications: {'peptide': 990} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 68, 'TRANS': 921} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 45 Conformer: "B" Number of residues, atoms: 990, 7798 Classifications: {'peptide': 990} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 68, 'TRANS': 921} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 45 bond proxies already assigned to first conformer: 7981 Chain: "B" Number of atoms: 7799 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 988, 7781 Classifications: {'peptide': 988} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 68, 'TRANS': 919} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 45 Conformer: "B" Number of residues, atoms: 988, 7781 Classifications: {'peptide': 988} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 68, 'TRANS': 919} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 45 bond proxies already assigned to first conformer: 7948 Time building chain proxies: 15.05, per 1000 atoms: 0.96 Number of scatterers: 15602 At special positions: 0 Unit cell: (96.96, 113.12, 150.49, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 98 16.00 O 2758 8.00 N 2834 7.00 C 9912 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.35 Conformation dependent library (CDL) restraints added in 5.6 seconds 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3780 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 14 sheets defined 66.9% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain 'A' and resid 220 through 235 removed outlier: 3.783A pdb=" N GLN A 224 " --> pdb=" O SER A 220 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA A 228 " --> pdb=" O GLN A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 252 Processing helix chain 'A' and resid 252 through 259 Processing helix chain 'A' and resid 260 through 272 removed outlier: 3.568A pdb=" N TYR A 264 " --> pdb=" O THR A 260 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU A 269 " --> pdb=" O ASN A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 291 removed outlier: 3.700A pdb=" N LEU A 280 " --> pdb=" O ALA A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 removed outlier: 4.099A pdb=" N ARG A 308 " --> pdb=" O GLN A 304 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN A 309 " --> pdb=" O CYS A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 326 removed outlier: 4.093A pdb=" N ILE A 316 " --> pdb=" O ASP A 312 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU A 326 " --> pdb=" O GLN A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 337 Processing helix chain 'A' and resid 340 through 354 Processing helix chain 'A' and resid 374 through 379 Processing helix chain 'A' and resid 392 through 410 Processing helix chain 'A' and resid 424 through 463 Processing helix chain 'A' and resid 467 through 474 removed outlier: 4.228A pdb=" N LEU A 474 " --> pdb=" O PHE A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 490 Processing helix chain 'A' and resid 496 through 521 Processing helix chain 'A' and resid 521 through 538 removed outlier: 3.674A pdb=" N ALA A 525 " --> pdb=" O GLY A 521 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU A 536 " --> pdb=" O LYS A 532 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU A 537 " --> pdb=" O TYR A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 557 Processing helix chain 'A' and resid 561 through 565 removed outlier: 3.655A pdb=" N GLU A 564 " --> pdb=" O ALA A 561 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLN A 565 " --> pdb=" O LEU A 562 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 561 through 565' Processing helix chain 'A' and resid 568 through 587 Processing helix chain 'A' and resid 624 through 635 Processing helix chain 'A' and resid 676 through 687 Processing helix chain 'A' and resid 688 through 705 removed outlier: 3.549A pdb=" N LEU A 692 " --> pdb=" O PRO A 688 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N GLY A 694 " --> pdb=" O THR A 690 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ALA A 695 " --> pdb=" O ALA A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 723 removed outlier: 3.640A pdb=" N ALA A 723 " --> pdb=" O GLN A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 750 Processing helix chain 'A' and resid 751 through 789 Processing helix chain 'A' and resid 818 through 824 Processing helix chain 'A' and resid 833 through 850 removed outlier: 4.532A pdb=" N LEU A 838 " --> pdb=" O GLY A 834 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N ASP A 839 " --> pdb=" O PRO A 835 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 867 Processing helix chain 'A' and resid 867 through 877 Processing helix chain 'A' and resid 883 through 888 removed outlier: 3.663A pdb=" N GLY A 887 " --> pdb=" O LYS A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 907 removed outlier: 3.963A pdb=" N ASN A 903 " --> pdb=" O MET A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 936 Processing helix chain 'A' and resid 937 through 944 Processing helix chain 'A' and resid 954 through 973 removed outlier: 3.726A pdb=" N GLY A 958 " --> pdb=" O ASP A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 981 Processing helix chain 'A' and resid 986 through 999 Processing helix chain 'A' and resid 1003 through 1017 removed outlier: 3.735A pdb=" N LEU A1017 " --> pdb=" O ARG A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1044 removed outlier: 3.795A pdb=" N GLN A1041 " --> pdb=" O PHE A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1044 through 1065 removed outlier: 3.868A pdb=" N ARG A1048 " --> pdb=" O PHE A1044 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA A1049 " --> pdb=" O SER A1045 " (cutoff:3.500A) Processing helix chain 'A' and resid 1111 through 1143 Proline residue: A1120 - end of helix Processing helix chain 'A' and resid 1159 through 1177 removed outlier: 3.636A pdb=" N GLU A1177 " --> pdb=" O ARG A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1191 Processing helix chain 'A' and resid 1197 through 1210 Processing helix chain 'A' and resid 1220 through 1225 removed outlier: 3.886A pdb=" N ARG A1224 " --> pdb=" O GLU A1220 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 237 Processing helix chain 'B' and resid 238 through 252 Processing helix chain 'B' and resid 252 through 259 Processing helix chain 'B' and resid 260 through 275 removed outlier: 3.666A pdb=" N TYR B 264 " --> pdb=" O THR B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 291 removed outlier: 3.724A pdb=" N LEU B 280 " --> pdb=" O ALA B 276 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY B 291 " --> pdb=" O VAL B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 309 removed outlier: 3.869A pdb=" N TYR B 299 " --> pdb=" O ASP B 295 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA B 301 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG B 308 " --> pdb=" O GLN B 304 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLN B 309 " --> pdb=" O CYS B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 325 removed outlier: 3.556A pdb=" N ILE B 316 " --> pdb=" O ASP B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 337 Processing helix chain 'B' and resid 340 through 354 removed outlier: 3.599A pdb=" N ALA B 345 " --> pdb=" O GLU B 341 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS B 353 " --> pdb=" O LYS B 349 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL B 354 " --> pdb=" O ALA B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 376 removed outlier: 4.282A pdb=" N ASP B 376 " --> pdb=" O LYS B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 410 Processing helix chain 'B' and resid 424 through 462 Processing helix chain 'B' and resid 467 through 474 removed outlier: 3.987A pdb=" N LEU B 474 " --> pdb=" O PHE B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 490 Processing helix chain 'B' and resid 497 through 521 Processing helix chain 'B' and resid 521 through 538 removed outlier: 3.708A pdb=" N ALA B 525 " --> pdb=" O GLY B 521 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU B 536 " --> pdb=" O LYS B 532 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU B 537 " --> pdb=" O TYR B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 556 Processing helix chain 'B' and resid 561 through 565 removed outlier: 3.802A pdb=" N GLN B 565 " --> pdb=" O LEU B 562 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 587 removed outlier: 3.543A pdb=" N THR B 587 " --> pdb=" O LEU B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 635 Processing helix chain 'B' and resid 676 through 687 Processing helix chain 'B' and resid 688 through 705 removed outlier: 3.507A pdb=" N LEU B 692 " --> pdb=" O PRO B 688 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA B 695 " --> pdb=" O ALA B 691 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N CYS B 705 " --> pdb=" O GLN B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 710 through 723 Processing helix chain 'B' and resid 751 through 789 Processing helix chain 'B' and resid 818 through 824 Processing helix chain 'B' and resid 836 through 850 Processing helix chain 'B' and resid 856 through 867 removed outlier: 3.614A pdb=" N LEU B 861 " --> pdb=" O LEU B 857 " (cutoff:3.500A) Processing helix chain 'B' and resid 867 through 877 Processing helix chain 'B' and resid 883 through 888 removed outlier: 3.618A pdb=" N GLY B 887 " --> pdb=" O LYS B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 890 through 907 Processing helix chain 'B' and resid 925 through 936 Processing helix chain 'B' and resid 937 through 944 Processing helix chain 'B' and resid 954 through 973 removed outlier: 3.755A pdb=" N GLY B 958 " --> pdb=" O ASP B 954 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 981 Processing helix chain 'B' and resid 986 through 999 removed outlier: 4.284A pdb=" N GLN B 992 " --> pdb=" O LYS B 988 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR B 993 " --> pdb=" O VAL B 989 " (cutoff:3.500A) Processing helix chain 'B' and resid 1003 through 1017 removed outlier: 3.727A pdb=" N ARG B1007 " --> pdb=" O ARG B1003 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU B1017 " --> pdb=" O ARG B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1024 through 1044 removed outlier: 3.613A pdb=" N GLN B1041 " --> pdb=" O PHE B1037 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLU B1042 " --> pdb=" O LYS B1038 " (cutoff:3.500A) Processing helix chain 'B' and resid 1044 through 1065 removed outlier: 3.604A pdb=" N ARG B1048 " --> pdb=" O PHE B1044 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TRP B1053 " --> pdb=" O ALA B1049 " (cutoff:3.500A) Processing helix chain 'B' and resid 1111 through 1143 removed outlier: 3.861A pdb=" N LYS B1116 " --> pdb=" O THR B1112 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ASN B1117 " --> pdb=" O ARG B1113 " (cutoff:3.500A) Proline residue: B1120 - end of helix Processing helix chain 'B' and resid 1159 through 1177 Processing helix chain 'B' and resid 1178 through 1192 Processing helix chain 'B' and resid 1197 through 1210 Processing helix chain 'B' and resid 1220 through 1225 removed outlier: 3.895A pdb=" N ARG B1224 " --> pdb=" O GLU B1220 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 411 through 415 Processing sheet with id=AA2, first strand: chain 'A' and resid 588 through 590 Processing sheet with id=AA3, first strand: chain 'A' and resid 607 through 609 Processing sheet with id=AA4, first strand: chain 'A' and resid 794 through 795 Processing sheet with id=AA5, first strand: chain 'A' and resid 798 through 800 Processing sheet with id=AA6, first strand: chain 'A' and resid 831 through 832 removed outlier: 4.442A pdb=" N ARG A 831 " --> pdb=" O SER A 915 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 919 through 921 Processing sheet with id=AA8, first strand: chain 'A' and resid 1069 through 1071 Processing sheet with id=AA9, first strand: chain 'B' and resid 411 through 415 Processing sheet with id=AB1, first strand: chain 'B' and resid 495 through 496 removed outlier: 3.592A pdb=" N LYS B 622 " --> pdb=" O TYR B 607 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 794 through 795 Processing sheet with id=AB3, first strand: chain 'B' and resid 798 through 799 Processing sheet with id=AB4, first strand: chain 'B' and resid 919 through 921 Processing sheet with id=AB5, first strand: chain 'B' and resid 1069 through 1071 957 hydrogen bonds defined for protein. 2825 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: 4.83 Time building geometry restraints manager: 6.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3565 1.33 - 1.45: 3217 1.45 - 1.57: 9055 1.57 - 1.69: 0 1.69 - 1.81: 148 Bond restraints: 15985 Sorted by residual: bond pdb=" N THR B 587 " pdb=" CA THR B 587 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.22e-02 6.72e+03 1.07e+01 bond pdb=" N TYR B 468 " pdb=" CA TYR B 468 " ideal model delta sigma weight residual 1.461 1.491 -0.030 9.20e-03 1.18e+04 1.03e+01 bond pdb=" N CYS B 591 " pdb=" CA CYS B 591 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.23e-02 6.61e+03 1.01e+01 bond pdb=" N LEU B 746 " pdb=" CA LEU B 746 " ideal model delta sigma weight residual 1.461 1.490 -0.029 9.20e-03 1.18e+04 9.72e+00 bond pdb=" N ARG A 601 " pdb=" CA ARG A 601 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.23e-02 6.61e+03 9.44e+00 ... (remaining 15980 not shown) Histogram of bond angle deviations from ideal: 99.35 - 106.41: 668 106.41 - 113.47: 8601 113.47 - 120.52: 6447 120.52 - 127.58: 5790 127.58 - 134.64: 212 Bond angle restraints: 21718 Sorted by residual: angle pdb=" CA GLY B 881 " pdb=" C GLY B 881 " pdb=" O GLY B 881 " ideal model delta sigma weight residual 122.28 118.28 4.00 1.00e+00 1.00e+00 1.60e+01 angle pdb=" C ARG B 805 " pdb=" N THR B 806 " pdb=" CA THR B 806 " ideal model delta sigma weight residual 120.90 126.49 -5.59 1.41e+00 5.03e-01 1.57e+01 angle pdb=" CG ARG A 598 " pdb=" CD ARG A 598 " pdb=" NE ARG A 598 " ideal model delta sigma weight residual 112.00 120.72 -8.72 2.20e+00 2.07e-01 1.57e+01 angle pdb=" N LEU B 593 " pdb=" CA LEU B 593 " pdb=" C LEU B 593 " ideal model delta sigma weight residual 110.30 104.46 5.84 1.50e+00 4.44e-01 1.52e+01 angle pdb=" N ALA B 750 " pdb=" CA ALA B 750 " pdb=" C ALA B 750 " ideal model delta sigma weight residual 111.28 107.13 4.15 1.09e+00 8.42e-01 1.45e+01 ... (remaining 21713 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 8762 17.50 - 34.99: 795 34.99 - 52.49: 168 52.49 - 69.99: 32 69.99 - 87.49: 17 Dihedral angle restraints: 9774 sinusoidal: 3962 harmonic: 5812 Sorted by residual: dihedral pdb=" C THR A1002 " pdb=" N THR A1002 " pdb=" CA THR A1002 " pdb=" CB THR A1002 " ideal model delta harmonic sigma weight residual -122.00 -131.26 9.26 0 2.50e+00 1.60e-01 1.37e+01 dihedral pdb=" C GLU B 442 " pdb=" N GLU B 442 " pdb=" CA GLU B 442 " pdb=" CB GLU B 442 " ideal model delta harmonic sigma weight residual -122.60 -114.02 -8.58 0 2.50e+00 1.60e-01 1.18e+01 dihedral pdb=" N LEU B 593 " pdb=" C LEU B 593 " pdb=" CA LEU B 593 " pdb=" CB LEU B 593 " ideal model delta harmonic sigma weight residual 122.80 114.84 7.96 0 2.50e+00 1.60e-01 1.01e+01 ... (remaining 9771 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 2065 0.090 - 0.181: 299 0.181 - 0.271: 37 0.271 - 0.362: 9 0.362 - 0.452: 1 Chirality restraints: 2411 Sorted by residual: chirality pdb=" CG LEU A 718 " pdb=" CB LEU A 718 " pdb=" CD1 LEU A 718 " pdb=" CD2 LEU A 718 " both_signs ideal model delta sigma weight residual False -2.59 -2.14 -0.45 2.00e-01 2.50e+01 5.11e+00 chirality pdb=" CA LEU B 593 " pdb=" N LEU B 593 " pdb=" C LEU B 593 " pdb=" CB LEU B 593 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" CB VAL B 867 " pdb=" CA VAL B 867 " pdb=" CG1 VAL B 867 " pdb=" CG2 VAL B 867 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.07e+00 ... (remaining 2408 not shown) Planarity restraints: 2829 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 434 " -0.022 2.00e-02 2.50e+03 4.34e-02 1.88e+01 pdb=" C LEU A 434 " 0.075 2.00e-02 2.50e+03 pdb=" O LEU A 434 " -0.028 2.00e-02 2.50e+03 pdb=" N LYS A 435 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 899 " -0.018 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C MET B 899 " 0.064 2.00e-02 2.50e+03 pdb=" O MET B 899 " -0.024 2.00e-02 2.50e+03 pdb=" N GLU B 900 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 680 " -0.016 2.00e-02 2.50e+03 2.79e-02 1.16e+01 pdb=" CG HIS A 680 " 0.057 2.00e-02 2.50e+03 pdb=" ND1 HIS A 680 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 HIS A 680 " -0.022 2.00e-02 2.50e+03 pdb=" CE1 HIS A 680 " 0.007 2.00e-02 2.50e+03 pdb=" NE2 HIS A 680 " -0.000 2.00e-02 2.50e+03 ... (remaining 2826 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 138 2.68 - 3.24: 14673 3.24 - 3.79: 26172 3.79 - 4.35: 34039 4.35 - 4.90: 54133 Nonbonded interactions: 129155 Sorted by model distance: nonbonded pdb=" CG LEU B 245 " pdb=" NE2 HIS B 249 " model vdw 2.128 3.550 nonbonded pdb=" CD2 LEU B 245 " pdb=" NE2 HIS B 249 " model vdw 2.135 3.540 nonbonded pdb=" CE1 HIS B 249 " pdb=" O GLY B 463 " model vdw 2.146 3.260 nonbonded pdb=" O LEU B 245 " pdb=" CD2 HIS B 249 " model vdw 2.240 3.260 nonbonded pdb=" OG SER A 220 " pdb=" OE1 GLN A 223 " model vdw 2.272 2.440 ... (remaining 129150 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 220 through 994 or resid 996 through 1050 or resid 1052 th \ rough 1062 or resid 1064 through 1230)) selection = (chain 'B' and (resid 220 through 994 or resid 996 through 1050 or resid 1052 th \ rough 1062 or resid 1064 through 1230)) } 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=0.03 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: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.190 Construct map_model_manager: 0.010 Extract box with map and model: 6.390 Check model and map are aligned: 0.240 Set scattering table: 0.140 Process input model: 51.900 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6507 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 : 0.007 0.082 15985 Z= 0.449 Angle : 1.022 9.639 21718 Z= 0.664 Chirality : 0.066 0.452 2411 Planarity : 0.007 0.057 2829 Dihedral : 14.297 87.486 5994 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % 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: 2.29 (0.18), residues: 1974 helix: 2.29 (0.14), residues: 1246 sheet: -0.06 (0.63), residues: 64 loop : 0.24 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A1154 HIS 0.038 0.003 HIS A 680 PHE 0.045 0.003 PHE A1119 TYR 0.022 0.002 TYR A 378 ARG 0.027 0.001 ARG B 450 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 379 time to evaluate : 1.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 LEU cc_start: 0.7497 (tt) cc_final: 0.7183 (mp) REVERT: A 299 TYR cc_start: 0.5476 (m-80) cc_final: 0.5006 (m-80) REVERT: A 436 THR cc_start: 0.8587 (m) cc_final: 0.8021 (p) REVERT: A 572 GLN cc_start: 0.7984 (mt0) cc_final: 0.7549 (mt0) REVERT: B 227 LEU cc_start: 0.5445 (tp) cc_final: 0.4758 (tp) REVERT: B 234 LEU cc_start: 0.5374 (mt) cc_final: 0.5139 (mp) REVERT: B 473 LEU cc_start: 0.7445 (mt) cc_final: 0.7111 (pp) REVERT: B 485 GLN cc_start: 0.5606 (mm-40) cc_final: 0.5382 (mm110) REVERT: B 618 ILE cc_start: 0.6219 (pt) cc_final: 0.5319 (mt) REVERT: B 784 SER cc_start: 0.6877 (m) cc_final: 0.6653 (t) REVERT: B 1043 MET cc_start: 0.6277 (mmm) cc_final: 0.5928 (ttm) REVERT: B 1076 VAL cc_start: 0.8298 (m) cc_final: 0.8022 (p) REVERT: B 1230 SER cc_start: 0.6469 (p) cc_final: 0.6178 (t) outliers start: 0 outliers final: 0 residues processed: 379 average time/residue: 0.3450 time to fit residues: 179.3450 Evaluate side-chains 183 residues out of total 1716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 1.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 166 optimal weight: 0.9980 chunk 149 optimal weight: 8.9990 chunk 82 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 114 optimal weight: 9.9990 chunk 178 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 485 GLN A 512 HIS A 585 GLN ** A 679 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 773 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 798 HIS A1035 GLN A1221 GLN B 515 GLN B 527 GLN B 529 HIS B 585 GLN B 588 GLN B 597 HIS ** B 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 812 HIS ** B 847 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 893 GLN ** B 920 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 972 GLN B1125 HIS B1209 GLN B1221 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6842 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15985 Z= 0.262 Angle : 0.641 11.413 21718 Z= 0.331 Chirality : 0.040 0.172 2411 Planarity : 0.005 0.040 2829 Dihedral : 4.124 24.342 2174 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.75 % Allowed : 10.00 % Favored : 88.25 % 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: 2.29 (0.18), residues: 1974 helix: 2.29 (0.14), residues: 1252 sheet: 0.14 (0.58), residues: 74 loop : 0.21 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A1154 HIS 0.019 0.002 HIS B 624 PHE 0.026 0.002 PHE B 863 TYR 0.017 0.002 TYR B 627 ARG 0.010 0.001 ARG A 450 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 194 time to evaluate : 1.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 227 LEU cc_start: 0.5092 (tp) cc_final: 0.4664 (tp) REVERT: B 306 MET cc_start: 0.5644 (mtt) cc_final: 0.5082 (mpp) REVERT: B 419 LYS cc_start: 0.7045 (tptt) cc_final: 0.6764 (tptp) REVERT: B 445 LEU cc_start: 0.8113 (mt) cc_final: 0.7894 (mp) REVERT: B 485 GLN cc_start: 0.5983 (mm-40) cc_final: 0.5433 (tt0) REVERT: B 585 GLN cc_start: 0.4845 (OUTLIER) cc_final: 0.4165 (pp30) REVERT: B 588 GLN cc_start: 0.6550 (mp-120) cc_final: 0.5993 (mp10) REVERT: B 784 SER cc_start: 0.7179 (m) cc_final: 0.6736 (t) REVERT: B 1043 MET cc_start: 0.6641 (mmm) cc_final: 0.6118 (ttm) REVERT: B 1076 VAL cc_start: 0.8306 (m) cc_final: 0.8060 (t) outliers start: 29 outliers final: 16 residues processed: 214 average time/residue: 0.2807 time to fit residues: 89.2279 Evaluate side-chains 164 residues out of total 1716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 147 time to evaluate : 1.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 800 MET Chi-restraints excluded: chain A residue 815 HIS Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 970 ASP Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain B residue 585 GLN Chi-restraints excluded: chain B residue 1050 ILE Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain B residue 1179 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 99 optimal weight: 9.9990 chunk 55 optimal weight: 0.9980 chunk 148 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 179 optimal weight: 7.9990 chunk 193 optimal weight: 9.9990 chunk 159 optimal weight: 0.6980 chunk 177 optimal weight: 5.9990 chunk 61 optimal weight: 0.8980 chunk 143 optimal weight: 9.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 HIS ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 HIS A 585 GLN B 238 GLN B 369 ASN B 390 HIS B 515 GLN ** B 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 597 HIS ** B 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 847 ASN ** B 920 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15985 Z= 0.223 Angle : 0.600 12.381 21718 Z= 0.301 Chirality : 0.038 0.165 2411 Planarity : 0.005 0.076 2829 Dihedral : 3.951 18.914 2174 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.63 % Allowed : 11.87 % Favored : 86.51 % 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: 2.25 (0.18), residues: 1974 helix: 2.25 (0.14), residues: 1251 sheet: 0.11 (0.59), residues: 64 loop : 0.22 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP B 441 HIS 0.019 0.001 HIS B 597 PHE 0.026 0.002 PHE B 863 TYR 0.016 0.001 TYR B 461 ARG 0.015 0.001 ARG B 411 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 155 time to evaluate : 1.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 306 MET cc_start: 0.5649 (mtt) cc_final: 0.5147 (mpp) REVERT: B 784 SER cc_start: 0.7520 (m) cc_final: 0.6869 (t) REVERT: B 866 GLU cc_start: 0.7508 (mm-30) cc_final: 0.7043 (tm-30) REVERT: B 873 ASP cc_start: 0.4997 (OUTLIER) cc_final: 0.4705 (m-30) REVERT: B 1043 MET cc_start: 0.6312 (mmm) cc_final: 0.5922 (ttm) REVERT: B 1076 VAL cc_start: 0.8483 (m) cc_final: 0.8241 (t) outliers start: 27 outliers final: 14 residues processed: 175 average time/residue: 0.2744 time to fit residues: 73.0463 Evaluate side-chains 157 residues out of total 1716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 142 time to evaluate : 1.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 800 MET Chi-restraints excluded: chain A residue 815 HIS Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1066 SER Chi-restraints excluded: chain B residue 873 ASP Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain B residue 1179 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 177 optimal weight: 2.9990 chunk 134 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 19 optimal weight: 0.1980 chunk 85 optimal weight: 2.9990 chunk 120 optimal weight: 6.9990 chunk 179 optimal weight: 8.9990 chunk 190 optimal weight: 0.9990 chunk 170 optimal weight: 9.9990 chunk 51 optimal weight: 0.0970 chunk 158 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 585 GLN A 829 GLN B 238 GLN B 252 GLN B 515 GLN ** B 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 745 HIS B 893 GLN ** B 920 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 moved from start: 0.4321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 15985 Z= 0.188 Angle : 0.555 9.955 21718 Z= 0.275 Chirality : 0.037 0.168 2411 Planarity : 0.004 0.039 2829 Dihedral : 3.875 18.685 2174 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.27 % Allowed : 12.95 % Favored : 85.78 % 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: 2.31 (0.19), residues: 1974 helix: 2.33 (0.14), residues: 1253 sheet: -0.08 (0.59), residues: 64 loop : 0.17 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP B1053 HIS 0.007 0.001 HIS A 680 PHE 0.020 0.002 PHE B 863 TYR 0.019 0.001 TYR B 461 ARG 0.005 0.000 ARG A 450 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 152 time to evaluate : 1.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 LYS cc_start: 0.7485 (OUTLIER) cc_final: 0.6825 (ptpp) REVERT: A 441 TRP cc_start: 0.7895 (m-10) cc_final: 0.7381 (m-10) REVERT: A 970 ASP cc_start: 0.7734 (OUTLIER) cc_final: 0.7498 (m-30) REVERT: B 268 MET cc_start: 0.6693 (ttm) cc_final: 0.6489 (tpp) REVERT: B 306 MET cc_start: 0.5508 (mtt) cc_final: 0.5212 (mtp) REVERT: B 784 SER cc_start: 0.7686 (m) cc_final: 0.6948 (p) REVERT: B 866 GLU cc_start: 0.7362 (mm-30) cc_final: 0.7045 (tm-30) REVERT: B 1043 MET cc_start: 0.6140 (mmm) cc_final: 0.5732 (ttm) REVERT: B 1076 VAL cc_start: 0.8561 (m) cc_final: 0.8308 (t) REVERT: B 1078 VAL cc_start: 0.6422 (t) cc_final: 0.6132 (t) REVERT: B 1132 MET cc_start: 0.8771 (tmm) cc_final: 0.8533 (tmm) outliers start: 21 outliers final: 17 residues processed: 167 average time/residue: 0.2643 time to fit residues: 68.0251 Evaluate side-chains 157 residues out of total 1716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 138 time to evaluate : 1.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 800 MET Chi-restraints excluded: chain A residue 815 HIS Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 920 HIS Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 970 ASP Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1007 ARG Chi-restraints excluded: chain A residue 1066 SER Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain B residue 1179 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 108 optimal weight: 9.9990 chunk 2 optimal weight: 0.9990 chunk 141 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 chunk 162 optimal weight: 20.0000 chunk 131 optimal weight: 0.0020 chunk 0 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 chunk 170 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 585 GLN B 238 GLN B 274 GLN B 515 GLN ** B 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 693 HIS ** B 920 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.4701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15985 Z= 0.177 Angle : 0.532 10.362 21718 Z= 0.264 Chirality : 0.037 0.152 2411 Planarity : 0.004 0.039 2829 Dihedral : 3.733 16.510 2174 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.57 % Allowed : 13.07 % Favored : 85.36 % 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: 2.47 (0.19), residues: 1974 helix: 2.44 (0.14), residues: 1258 sheet: -0.09 (0.59), residues: 64 loop : 0.26 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B1053 HIS 0.012 0.001 HIS B 249 PHE 0.018 0.001 PHE B 721 TYR 0.016 0.001 TYR B 627 ARG 0.004 0.000 ARG A 411 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 147 time to evaluate : 1.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 LYS cc_start: 0.7667 (OUTLIER) cc_final: 0.7019 (ptpp) REVERT: A 868 MET cc_start: 0.8415 (tpp) cc_final: 0.7874 (tpp) REVERT: B 268 MET cc_start: 0.6814 (ttm) cc_final: 0.6565 (tpp) REVERT: B 306 MET cc_start: 0.5477 (mtt) cc_final: 0.5234 (mtp) REVERT: B 322 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7363 (pm20) REVERT: B 445 LEU cc_start: 0.8327 (mt) cc_final: 0.8049 (mp) REVERT: B 573 MET cc_start: 0.6219 (tpp) cc_final: 0.5855 (tpp) REVERT: B 640 THR cc_start: 0.7243 (p) cc_final: 0.6993 (p) REVERT: B 784 SER cc_start: 0.7728 (m) cc_final: 0.6984 (p) REVERT: B 1043 MET cc_start: 0.6283 (mmm) cc_final: 0.5813 (ttm) REVERT: B 1047 THR cc_start: 0.6248 (t) cc_final: 0.5995 (t) REVERT: B 1076 VAL cc_start: 0.8619 (m) cc_final: 0.8399 (t) REVERT: B 1078 VAL cc_start: 0.6408 (t) cc_final: 0.6082 (t) REVERT: B 1132 MET cc_start: 0.8815 (tmm) cc_final: 0.8565 (tmm) REVERT: B 1163 MET cc_start: 0.8553 (ttp) cc_final: 0.8245 (ttp) outliers start: 26 outliers final: 14 residues processed: 167 average time/residue: 0.2430 time to fit residues: 63.4326 Evaluate side-chains 148 residues out of total 1716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 132 time to evaluate : 1.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 815 HIS Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1066 SER Chi-restraints excluded: chain B residue 322 GLN Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain B residue 1179 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 171 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 111 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 chunk 190 optimal weight: 0.9990 chunk 158 optimal weight: 0.0570 chunk 88 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 chunk 183 optimal weight: 9.9990 overall best weight: 1.5704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 GLN ** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 953 GLN B 238 GLN B 515 GLN ** B 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 829 GLN B 920 HIS ** B1080 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.5251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15985 Z= 0.271 Angle : 0.588 9.120 21718 Z= 0.294 Chirality : 0.039 0.212 2411 Planarity : 0.005 0.039 2829 Dihedral : 3.930 17.896 2174 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.11 % Allowed : 12.89 % Favored : 85.00 % 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: 2.24 (0.19), residues: 1974 helix: 2.29 (0.14), residues: 1251 sheet: -0.19 (0.53), residues: 74 loop : 0.13 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B1053 HIS 0.015 0.001 HIS B 249 PHE 0.029 0.002 PHE B 863 TYR 0.024 0.002 TYR B 461 ARG 0.007 0.001 ARG A 411 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 142 time to evaluate : 1.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 LYS cc_start: 0.7779 (OUTLIER) cc_final: 0.7114 (ptpp) REVERT: A 499 THR cc_start: 0.7583 (p) cc_final: 0.7333 (t) REVERT: A 1007 ARG cc_start: 0.6199 (OUTLIER) cc_final: 0.5641 (ttt-90) REVERT: A 1113 ARG cc_start: 0.6367 (mtm180) cc_final: 0.6028 (ttp-110) REVERT: B 249 HIS cc_start: 0.5968 (OUTLIER) cc_final: 0.5755 (t-90) REVERT: B 286 MET cc_start: 0.4213 (mmt) cc_final: 0.3934 (mpp) REVERT: B 306 MET cc_start: 0.5765 (mtt) cc_final: 0.5460 (mtp) REVERT: B 322 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7296 (pm20) REVERT: B 573 MET cc_start: 0.6150 (tpp) cc_final: 0.5772 (tpp) REVERT: B 578 LEU cc_start: 0.7463 (tp) cc_final: 0.6991 (tp) REVERT: B 784 SER cc_start: 0.7842 (m) cc_final: 0.7046 (p) REVERT: B 863 PHE cc_start: 0.5463 (t80) cc_final: 0.5186 (t80) REVERT: B 1043 MET cc_start: 0.6283 (mmm) cc_final: 0.5827 (ttm) REVERT: B 1047 THR cc_start: 0.6271 (t) cc_final: 0.6017 (t) REVERT: B 1076 VAL cc_start: 0.8717 (m) cc_final: 0.8487 (t) REVERT: B 1132 MET cc_start: 0.8835 (tmm) cc_final: 0.8571 (tmm) REVERT: B 1163 MET cc_start: 0.8600 (ttp) cc_final: 0.8246 (ttp) outliers start: 35 outliers final: 22 residues processed: 165 average time/residue: 0.2824 time to fit residues: 69.7198 Evaluate side-chains 156 residues out of total 1716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 130 time to evaluate : 1.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 800 MET Chi-restraints excluded: chain A residue 815 HIS Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 920 HIS Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 965 VAL Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1007 ARG Chi-restraints excluded: chain A residue 1066 SER Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 322 GLN Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain B residue 1112 THR Chi-restraints excluded: chain B residue 1179 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 21 optimal weight: 0.8980 chunk 108 optimal weight: 20.0000 chunk 139 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 160 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 189 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 115 optimal weight: 0.0040 chunk 87 optimal weight: 0.8980 chunk 117 optimal weight: 0.8980 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 515 GLN ** B 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7039 moved from start: 0.5403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15985 Z= 0.180 Angle : 0.547 9.757 21718 Z= 0.272 Chirality : 0.037 0.217 2411 Planarity : 0.004 0.047 2829 Dihedral : 3.788 19.641 2174 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.33 % Allowed : 13.31 % Favored : 85.36 % 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: 2.31 (0.19), residues: 1974 helix: 2.39 (0.14), residues: 1249 sheet: -0.16 (0.54), residues: 74 loop : 0.08 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B1053 HIS 0.016 0.001 HIS B 249 PHE 0.018 0.001 PHE B 863 TYR 0.016 0.001 TYR B 461 ARG 0.014 0.000 ARG A 770 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 137 time to evaluate : 1.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 LYS cc_start: 0.7772 (OUTLIER) cc_final: 0.7055 (ptpp) REVERT: A 868 MET cc_start: 0.8422 (tpp) cc_final: 0.7986 (tpp) REVERT: A 1007 ARG cc_start: 0.5998 (OUTLIER) cc_final: 0.5276 (ttt-90) REVERT: A 1213 LYS cc_start: 0.8858 (mmmt) cc_final: 0.8558 (mmtm) REVERT: B 249 HIS cc_start: 0.5923 (t-170) cc_final: 0.5653 (t-90) REVERT: B 286 MET cc_start: 0.3938 (mmt) cc_final: 0.3485 (mpp) REVERT: B 306 MET cc_start: 0.5607 (mtt) cc_final: 0.5329 (mtp) REVERT: B 322 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7334 (pm20) REVERT: B 573 MET cc_start: 0.6036 (tpp) cc_final: 0.5616 (tpp) REVERT: B 784 SER cc_start: 0.7829 (m) cc_final: 0.7047 (p) REVERT: B 863 PHE cc_start: 0.5388 (t80) cc_final: 0.5086 (t80) REVERT: B 1043 MET cc_start: 0.6254 (mmm) cc_final: 0.5817 (ttm) REVERT: B 1047 THR cc_start: 0.6318 (t) cc_final: 0.6070 (t) REVERT: B 1076 VAL cc_start: 0.8767 (m) cc_final: 0.8501 (p) REVERT: B 1132 MET cc_start: 0.8818 (tmm) cc_final: 0.8593 (tmm) REVERT: B 1163 MET cc_start: 0.8566 (ttp) cc_final: 0.8199 (ttp) outliers start: 22 outliers final: 16 residues processed: 153 average time/residue: 0.2465 time to fit residues: 58.7827 Evaluate side-chains 143 residues out of total 1716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 124 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 800 MET Chi-restraints excluded: chain A residue 815 HIS Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 920 HIS Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1007 ARG Chi-restraints excluded: chain A residue 1066 SER Chi-restraints excluded: chain B residue 322 GLN Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain B residue 1179 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 75 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 17 optimal weight: 0.4980 chunk 149 optimal weight: 0.8980 chunk 172 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 515 GLN ** B1080 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.5585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15985 Z= 0.188 Angle : 0.547 10.093 21718 Z= 0.270 Chirality : 0.037 0.193 2411 Planarity : 0.004 0.039 2829 Dihedral : 3.776 18.321 2174 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.33 % Allowed : 13.80 % Favored : 84.88 % 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: 2.29 (0.19), residues: 1974 helix: 2.39 (0.14), residues: 1249 sheet: -0.17 (0.55), residues: 74 loop : 0.04 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B1053 HIS 0.014 0.001 HIS B 249 PHE 0.018 0.001 PHE B 863 TYR 0.020 0.001 TYR B 627 ARG 0.008 0.000 ARG A 770 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 130 time to evaluate : 1.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 LYS cc_start: 0.7735 (OUTLIER) cc_final: 0.7107 (ptpp) REVERT: A 621 LEU cc_start: 0.7779 (mt) cc_final: 0.7565 (mp) REVERT: A 1007 ARG cc_start: 0.5940 (OUTLIER) cc_final: 0.5421 (ttt-90) REVERT: A 1113 ARG cc_start: 0.6315 (mtm180) cc_final: 0.5949 (ttp-110) REVERT: A 1213 LYS cc_start: 0.8951 (mmmt) cc_final: 0.8617 (mmmm) REVERT: B 249 HIS cc_start: 0.5987 (OUTLIER) cc_final: 0.5689 (t-90) REVERT: B 286 MET cc_start: 0.4171 (mmt) cc_final: 0.3755 (mpp) REVERT: B 306 MET cc_start: 0.5632 (mtt) cc_final: 0.5429 (mtp) REVERT: B 322 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7329 (pm20) REVERT: B 573 MET cc_start: 0.6113 (tpp) cc_final: 0.5797 (tpp) REVERT: B 784 SER cc_start: 0.7856 (m) cc_final: 0.7058 (p) REVERT: B 863 PHE cc_start: 0.5496 (t80) cc_final: 0.5167 (t80) REVERT: B 1043 MET cc_start: 0.6299 (mmm) cc_final: 0.5853 (ttm) REVERT: B 1047 THR cc_start: 0.6215 (t) cc_final: 0.5981 (t) REVERT: B 1076 VAL cc_start: 0.8801 (m) cc_final: 0.8528 (p) REVERT: B 1163 MET cc_start: 0.8589 (ttp) cc_final: 0.8219 (ttp) outliers start: 22 outliers final: 15 residues processed: 145 average time/residue: 0.2647 time to fit residues: 58.8013 Evaluate side-chains 144 residues out of total 1716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 125 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 800 MET Chi-restraints excluded: chain A residue 815 HIS Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 920 HIS Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1007 ARG Chi-restraints excluded: chain A residue 1066 SER Chi-restraints excluded: chain B residue 249 HIS Chi-restraints excluded: chain B residue 322 GLN Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain B residue 1179 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 181 optimal weight: 2.9990 chunk 165 optimal weight: 4.9990 chunk 176 optimal weight: 0.9990 chunk 106 optimal weight: 20.0000 chunk 77 optimal weight: 0.7980 chunk 138 optimal weight: 1.9990 chunk 54 optimal weight: 0.0980 chunk 159 optimal weight: 3.9990 chunk 167 optimal weight: 4.9990 chunk 116 optimal weight: 6.9990 chunk 187 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 515 GLN ** B 680 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1080 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.5982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15985 Z= 0.241 Angle : 0.585 9.662 21718 Z= 0.291 Chirality : 0.039 0.192 2411 Planarity : 0.004 0.039 2829 Dihedral : 3.893 17.807 2174 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.45 % Allowed : 13.67 % Favored : 84.88 % 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: 2.15 (0.19), residues: 1974 helix: 2.27 (0.14), residues: 1250 sheet: -0.22 (0.55), residues: 74 loop : 0.01 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B1053 HIS 0.013 0.001 HIS B 249 PHE 0.018 0.002 PHE B 497 TYR 0.021 0.001 TYR B 627 ARG 0.006 0.000 ARG A 770 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 134 time to evaluate : 1.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 LYS cc_start: 0.7737 (OUTLIER) cc_final: 0.7128 (ptpp) REVERT: A 500 LEU cc_start: 0.9092 (tt) cc_final: 0.8877 (tp) REVERT: A 1007 ARG cc_start: 0.6205 (OUTLIER) cc_final: 0.5597 (ttt-90) REVERT: A 1113 ARG cc_start: 0.6527 (mtm180) cc_final: 0.6267 (ttp-110) REVERT: A 1213 LYS cc_start: 0.8996 (mmmt) cc_final: 0.8750 (mmmm) REVERT: B 286 MET cc_start: 0.4103 (mmt) cc_final: 0.3725 (mpp) REVERT: B 306 MET cc_start: 0.5617 (mtt) cc_final: 0.5396 (mtp) REVERT: B 322 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.7161 (pm20) REVERT: B 573 MET cc_start: 0.6182 (tpp) cc_final: 0.5863 (tpp) REVERT: B 784 SER cc_start: 0.7849 (m) cc_final: 0.7059 (p) REVERT: B 863 PHE cc_start: 0.5598 (t80) cc_final: 0.5214 (t80) REVERT: B 1043 MET cc_start: 0.6448 (mmm) cc_final: 0.5983 (ttm) REVERT: B 1047 THR cc_start: 0.6348 (t) cc_final: 0.6118 (t) REVERT: B 1076 VAL cc_start: 0.8834 (m) cc_final: 0.8604 (p) REVERT: B 1163 MET cc_start: 0.8607 (ttp) cc_final: 0.8235 (ttp) outliers start: 24 outliers final: 17 residues processed: 151 average time/residue: 0.2598 time to fit residues: 60.4688 Evaluate side-chains 142 residues out of total 1716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 122 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 800 MET Chi-restraints excluded: chain A residue 815 HIS Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 920 HIS Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1007 ARG Chi-restraints excluded: chain A residue 1066 SER Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain B residue 322 GLN Chi-restraints excluded: chain B residue 718 LEU Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain B residue 1179 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 114 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 chunk 196 optimal weight: 0.0060 chunk 180 optimal weight: 1.9990 chunk 156 optimal weight: 0.9990 chunk 16 optimal weight: 0.0770 chunk 120 optimal weight: 2.9990 chunk 95 optimal weight: 0.0770 chunk 124 optimal weight: 6.9990 chunk 166 optimal weight: 2.9990 overall best weight: 0.3712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.6059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 15985 Z= 0.161 Angle : 0.550 12.094 21718 Z= 0.271 Chirality : 0.036 0.190 2411 Planarity : 0.004 0.040 2829 Dihedral : 3.732 18.478 2174 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.20 % Allowed : 14.16 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.19), residues: 1974 helix: 2.43 (0.14), residues: 1253 sheet: -0.15 (0.56), residues: 74 loop : 0.03 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP B1053 HIS 0.015 0.001 HIS B 249 PHE 0.018 0.001 PHE B 863 TYR 0.017 0.001 TYR B 627 ARG 0.006 0.000 ARG A 770 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3948 Ramachandran restraints generated. 1974 Oldfield, 0 Emsley, 1974 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 133 time to evaluate : 1.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 278 LYS cc_start: 0.7768 (OUTLIER) cc_final: 0.7568 (pttt) REVERT: A 456 LEU cc_start: 0.8552 (mt) cc_final: 0.8273 (mt) REVERT: A 500 LEU cc_start: 0.8966 (tt) cc_final: 0.8730 (tp) REVERT: A 1007 ARG cc_start: 0.5873 (OUTLIER) cc_final: 0.5418 (ttt-90) REVERT: A 1113 ARG cc_start: 0.6448 (mtm180) cc_final: 0.6158 (ttp-110) REVERT: A 1128 ASP cc_start: 0.7196 (m-30) cc_final: 0.6987 (m-30) REVERT: A 1213 LYS cc_start: 0.8998 (mmmt) cc_final: 0.8773 (mmmm) REVERT: B 286 MET cc_start: 0.4079 (mmt) cc_final: 0.3700 (mpp) REVERT: B 322 GLN cc_start: 0.8031 (OUTLIER) cc_final: 0.7216 (pm20) REVERT: B 445 LEU cc_start: 0.8234 (mt) cc_final: 0.8023 (mp) REVERT: B 573 MET cc_start: 0.6329 (tpp) cc_final: 0.5997 (tpp) REVERT: B 784 SER cc_start: 0.7830 (m) cc_final: 0.7039 (p) REVERT: B 863 PHE cc_start: 0.5643 (t80) cc_final: 0.5284 (t80) REVERT: B 1043 MET cc_start: 0.6479 (mmm) cc_final: 0.6068 (ttm) REVERT: B 1076 VAL cc_start: 0.8833 (m) cc_final: 0.8616 (p) REVERT: B 1163 MET cc_start: 0.8558 (ttp) cc_final: 0.8197 (ttp) outliers start: 20 outliers final: 16 residues processed: 147 average time/residue: 0.2548 time to fit residues: 57.6649 Evaluate side-chains 149 residues out of total 1716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 130 time to evaluate : 1.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 498 THR Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 800 MET Chi-restraints excluded: chain A residue 815 HIS Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 920 HIS Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1007 ARG Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain B residue 322 GLN Chi-restraints excluded: chain B residue 404 LEU Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain B residue 1179 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 47 optimal weight: 0.7980 chunk 144 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 156 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 160 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 137 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1080 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 = 0.4237 r_free = 0.4237 target = 0.157430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.136167 restraints weight = 71671.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.132873 restraints weight = 66133.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.130376 restraints weight = 54849.156| |-----------------------------------------------------------------------------| r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3860 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3860 r_free = 0.3860 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3859 r_free = 0.3859 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3859 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.6206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15985 Z= 0.209 Angle : 0.569 11.320 21718 Z= 0.282 Chirality : 0.038 0.193 2411 Planarity : 0.004 0.040 2829 Dihedral : 3.776 19.030 2174 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.27 % Allowed : 14.34 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.19), residues: 1974 helix: 2.40 (0.14), residues: 1253 sheet: -0.23 (0.55), residues: 74 loop : 0.02 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B1053 HIS 0.009 0.001 HIS B 249 PHE 0.017 0.002 PHE B 721 TYR 0.019 0.001 TYR B 627 ARG 0.006 0.000 ARG A 770 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2903.56 seconds wall clock time: 56 minutes 16.55 seconds (3376.55 seconds total)