Starting phenix.real_space_refine on Mon Nov 20 18:05:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pzp_13735/11_2023/7pzp_13735.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pzp_13735/11_2023/7pzp_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_13735/11_2023/7pzp_13735.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pzp_13735/11_2023/7pzp_13735.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pzp_13735/11_2023/7pzp_13735.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pzp_13735/11_2023/7pzp_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-1.21rc1-5144/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: 5.67 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: 1.99 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: 5.68 Time building geometry restraints manager: 6.28 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: 1.560 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: 0.020 Extract box with map and model: 6.480 Check model and map are aligned: 0.240 Set scattering table: 0.140 Process input model: 54.360 Find NCS groups from input model: 1.280 Set up NCS constraints: 0.120 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:3.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.820 ------------------------------------------------------------------------------- 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 *********************** 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 : 2.192 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 outliers start: 0 outliers final: 0 residues processed: 379 average time/residue: 0.3793 time to fit residues: 197.9275 Evaluate side-chains 176 residues out of total 1716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 1.824 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6588 ------------------------------------------------------------------------------- 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: 5.9990 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 572 GLN 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 972 GLN B1125 HIS B1209 GLN B1221 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 moved from start: 0.3090 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= 0.268 Angle : 0.651 11.515 21718 Z= 0.336 Chirality : 0.041 0.177 2411 Planarity : 0.005 0.039 2829 Dihedral : 4.100 23.995 2174 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.05 % Allowed : 9.58 % Favored : 88.37 % 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: 2.30 (0.14), residues: 1249 sheet: 0.14 (0.57), residues: 74 loop : 0.18 (0.24), residues: 651 *********************** 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 221 residues out of total 1716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 187 time to evaluate : 1.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 17 residues processed: 211 average time/residue: 0.2965 time to fit residues: 92.9520 Evaluate side-chains 162 residues out of total 1716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 145 time to evaluate : 1.889 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1709 time to fit residues: 7.8620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 99 optimal weight: 8.9990 chunk 55 optimal weight: 2.9990 chunk 148 optimal weight: 0.7980 chunk 121 optimal weight: 5.9990 chunk 49 optimal weight: 0.6980 chunk 179 optimal weight: 0.9980 chunk 193 optimal weight: 7.9990 chunk 159 optimal weight: 1.9990 chunk 177 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 143 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 HIS A 572 GLN 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 616 GLN ** B 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 847 ASN B 893 GLN ** B 920 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 moved from start: 0.3852 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: