Starting phenix.real_space_refine (version: dev) on Mon Dec 12 14:02:56 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7j_9935/12_2022/6k7j_9935_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7j_9935/12_2022/6k7j_9935.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7j_9935/12_2022/6k7j_9935.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7j_9935/12_2022/6k7j_9935.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7j_9935/12_2022/6k7j_9935_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k7j_9935/12_2022/6k7j_9935_updated.pdb" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 35": "OE1" <-> "OE2" Residue "A ARG 67": "NH1" <-> "NH2" Residue "A PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 92": "OD1" <-> "OD2" Residue "A TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 119": "OE1" <-> "OE2" Residue "A GLU 176": "OE1" <-> "OE2" Residue "A TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A ASP 208": "OD1" <-> "OD2" Residue "A ASP 210": "OD1" <-> "OD2" Residue "A TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 230": "OD1" <-> "OD2" Residue "A PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 445": "OD1" <-> "OD2" Residue "A TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 533": "OE1" <-> "OE2" Residue "A TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 601": "OE1" <-> "OE2" Residue "A TYR 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 745": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 786": "OD1" <-> "OD2" Residue "A TYR 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 824": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 848": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 863": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 885": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 896": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 908": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 926": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 950": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 962": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 968": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 972": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 991": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1031": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 225": "OE1" <-> "OE2" Residue "C PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 305": "OD1" <-> "OD2" Residue "C TYR 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 10602 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 986, 7853 Classifications: {'peptide': 986} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 955} Chain breaks: 3 Chain: "C" Number of atoms: 2615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2615 Classifications: {'peptide': 325} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 299} Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ACP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {'NAG': 2, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.55, per 1000 atoms: 0.62 Number of scatterers: 10602 At special positions: 0 Unit cell: (73.87, 116.2, 166.83, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 56 16.00 P 3 15.00 Mg 1 11.99 O 1922 8.00 N 1757 7.00 C 6863 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS C 91 " - pdb=" SG CYS C 104 " distance=2.03 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 102 " distance=2.02 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 171 " distance=2.05 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 Links applied ALPHA1-4 " NAG B 2 " - " MAN B 3 " BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG B 1 " - " ASN C 180 " " NAG C 401 " - " ASN C 294 " " NAG C 402 " - " ASN C 107 " Time building additional restraints: 4.63 Conformation dependent library (CDL) restraints added in 1.7 seconds 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2468 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 51 helices and 8 sheets defined 40.7% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'A' and resid 64 through 73 removed outlier: 3.985A pdb=" N TYR A 70 " --> pdb=" O PRO A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 89 removed outlier: 4.233A pdb=" N GLN A 89 " --> pdb=" O ALA A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 122 Processing helix chain 'A' and resid 128 through 131 No H-bonds generated for 'chain 'A' and resid 128 through 131' Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 209 through 212 No H-bonds generated for 'chain 'A' and resid 209 through 212' Processing helix chain 'A' and resid 271 through 273 No H-bonds generated for 'chain 'A' and resid 271 through 273' Processing helix chain 'A' and resid 275 through 278 No H-bonds generated for 'chain 'A' and resid 275 through 278' Processing helix chain 'A' and resid 289 through 322 Processing helix chain 'A' and resid 340 through 354 removed outlier: 5.367A pdb=" N ASN A 353 " --> pdb=" O ILE A 349 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LEU A 354 " --> pdb=" O LEU A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 376 Processing helix chain 'A' and resid 394 through 396 No H-bonds generated for 'chain 'A' and resid 394 through 396' Processing helix chain 'A' and resid 399 through 401 No H-bonds generated for 'chain 'A' and resid 399 through 401' Processing helix chain 'A' and resid 451 through 454 No H-bonds generated for 'chain 'A' and resid 451 through 454' Processing helix chain 'A' and resid 459 through 471 removed outlier: 4.810A pdb=" N GLU A 464 " --> pdb=" O PRO A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 499 Processing helix chain 'A' and resid 560 through 564 Processing helix chain 'A' and resid 571 through 587 removed outlier: 5.120A pdb=" N ILE A 576 " --> pdb=" O LYS A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 615 removed outlier: 4.635A pdb=" N GLU A 606 " --> pdb=" O SER A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 632 Processing helix chain 'A' and resid 652 through 661 Processing helix chain 'A' and resid 674 through 683 Processing helix chain 'A' and resid 731 through 737 removed outlier: 4.143A pdb=" N TYR A 736 " --> pdb=" O LYS A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 752 Processing helix chain 'A' and resid 763 through 777 removed outlier: 4.191A pdb=" N GLN A 776 " --> pdb=" O MET A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 796 Processing helix chain 'A' and resid 810 through 813 No H-bonds generated for 'chain 'A' and resid 810 through 813' Processing helix chain 'A' and resid 822 through 830 removed outlier: 3.748A pdb=" N LYS A 826 " --> pdb=" O LYS A 823 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU A 829 " --> pdb=" O LYS A 826 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N MET A 830 " --> pdb=" O ASN A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 865 removed outlier: 4.313A pdb=" N ILE A 857 " --> pdb=" O VAL A 853 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLU A 858 " --> pdb=" O LEU A 854 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ILE A 859 " --> pdb=" O TYR A 855 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N VAL A 864 " --> pdb=" O TRP A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 880 Processing helix chain 'A' and resid 887 through 895 removed outlier: 4.134A pdb=" N LEU A 891 " --> pdb=" O ALA A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 907 Processing helix chain 'A' and resid 909 through 911 No H-bonds generated for 'chain 'A' and resid 909 through 911' Processing helix chain 'A' and resid 913 through 916 No H-bonds generated for 'chain 'A' and resid 913 through 916' Processing helix chain 'A' and resid 923 through 947 Proline residue: A 944 - end of helix Processing helix chain 'A' and resid 962 through 984 Processing helix chain 'A' and resid 990 through 1010 Processing helix chain 'A' and resid 1021 through 1023 No H-bonds generated for 'chain 'A' and resid 1021 through 1023' Processing helix chain 'A' and resid 1026 through 1032 Processing helix chain 'A' and resid 1036 through 1061 removed outlier: 4.145A pdb=" N LEU A1041 " --> pdb=" O TRP A1037 " (cutoff:3.500A) Proline residue: A1044 - end of helix removed outlier: 5.196A pdb=" N LEU A1050 " --> pdb=" O ALA A1046 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ASP A1051 " --> pdb=" O SER A1047 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 73 removed outlier: 3.919A pdb=" N LEU C 59 " --> pdb=" O PHE C 55 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ILE C 62 " --> pdb=" O GLY C 58 " (cutoff:3.500A) Proline residue: C 63 - end of helix Processing helix chain 'C' and resid 132 through 135 No H-bonds generated for 'chain 'C' and resid 132 through 135' Processing helix chain 'C' and resid 140 through 144 Processing helix chain 'C' and resid 147 through 151 Processing helix chain 'C' and resid 173 through 176 No H-bonds generated for 'chain 'C' and resid 173 through 176' Processing helix chain 'C' and resid 207 through 211 Processing helix chain 'C' and resid 223 through 226 No H-bonds generated for 'chain 'C' and resid 223 through 226' Processing helix chain 'C' and resid 240 through 242 No H-bonds generated for 'chain 'C' and resid 240 through 242' Processing helix chain 'C' and resid 251 through 253 No H-bonds generated for 'chain 'C' and resid 251 through 253' Processing helix chain 'C' and resid 255 through 261 Processing helix chain 'C' and resid 324 through 349 Processing sheet with id= A, first strand: chain 'A' and resid 156 through 159 removed outlier: 7.150A pdb=" N ASP A 168 " --> pdb=" O VAL A 268 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 181 through 184 removed outlier: 3.904A pdb=" N CYS A 181 " --> pdb=" O ARG A 197 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 219 through 221 Processing sheet with id= D, first strand: chain 'A' and resid 693 through 696 removed outlier: 7.312A pdb=" N ALA A 726 " --> pdb=" O ILE A 694 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ILE A 696 " --> pdb=" O ALA A 726 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE A 728 " --> pdb=" O ILE A 696 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ALA A 755 " --> pdb=" O LEU A 727 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N ILE A 729 " --> pdb=" O ALA A 755 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N ILE A 757 " --> pdb=" O ILE A 729 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE A 666 " --> pdb=" O VAL A 756 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N CYS A 758 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ILE A 668 " --> pdb=" O CYS A 758 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N VAL A 780 " --> pdb=" O LYS A 404 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ILE A 406 " --> pdb=" O VAL A 780 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU A 782 " --> pdb=" O ILE A 406 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N SER A 408 " --> pdb=" O LEU A 782 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ILE A 784 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL A 799 " --> pdb=" O ALA A 783 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N GLY A 785 " --> pdb=" O VAL A 799 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL A 801 " --> pdb=" O GLY A 785 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N TYR A 817 " --> pdb=" O GLY A 802 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 506 through 508 removed outlier: 3.516A pdb=" N VAL A 515 " --> pdb=" O THR A 508 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP A 518 " --> pdb=" O GLN A 522 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLN A 522 " --> pdb=" O ASP A 518 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 540 through 545 removed outlier: 3.678A pdb=" N LEU A 592 " --> pdb=" O THR A 642 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N GLU A 645 " --> pdb=" O PHE A 421 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N PHE A 421 " --> pdb=" O GLU A 645 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 77 through 81 removed outlier: 5.881A pdb=" N TYR C 122 " --> pdb=" O LEU C 272 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N LEU C 272 " --> pdb=" O TYR C 122 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU C 124 " --> pdb=" O ARG C 270 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N ARG C 270 " --> pdb=" O LEU C 124 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 106 through 109 removed outlier: 4.722A pdb=" N ARG C 290 " --> pdb=" O ILE C 188 " (cutoff:3.500A) 380 hydrogen bonds defined for protein. 1098 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.46 Time building geometry restraints manager: 4.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1885 1.32 - 1.45: 2830 1.45 - 1.57: 6044 1.57 - 1.69: 6 1.69 - 1.82: 87 Bond restraints: 10852 Sorted by residual: bond pdb=" O2B ACP A1201 " pdb=" PB ACP A1201 " ideal model delta sigma weight residual 1.507 1.607 -0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" O3A ACP A1201 " pdb=" PB ACP A1201 " ideal model delta sigma weight residual 1.698 1.606 0.092 2.00e-02 2.50e+03 2.10e+01 bond pdb=" C4 ACP A1201 " pdb=" C5 ACP A1201 " ideal model delta sigma weight residual 1.386 1.465 -0.079 2.00e-02 2.50e+03 1.54e+01 bond pdb=" O3G ACP A1201 " pdb=" PG ACP A1201 " ideal model delta sigma weight residual 1.532 1.605 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" CD LYS C 308 " pdb=" CE LYS C 308 " ideal model delta sigma weight residual 1.520 1.413 0.107 3.00e-02 1.11e+03 1.28e+01 ... (remaining 10847 not shown) Histogram of bond angle deviations from ideal: 97.91 - 105.52: 222 105.52 - 113.13: 5794 113.13 - 120.73: 5114 120.73 - 128.34: 3503 128.34 - 135.95: 104 Bond angle restraints: 14737 Sorted by residual: angle pdb=" N ASP A 672 " pdb=" CA ASP A 672 " pdb=" C ASP A 672 " ideal model delta sigma weight residual 113.18 120.61 -7.43 1.33e+00 5.65e-01 3.12e+01 angle pdb=" C PRO A 91 " pdb=" N ASP A 92 " pdb=" CA ASP A 92 " ideal model delta sigma weight residual 121.54 132.00 -10.46 1.91e+00 2.74e-01 3.00e+01 angle pdb=" C2 NAG C 401 " pdb=" C1 NAG C 401 " pdb=" O5 NAG C 401 " ideal model delta sigma weight residual 109.64 112.54 -2.90 5.38e-01 3.45e+00 2.91e+01 angle pdb=" CA LEU A 738 " pdb=" CB LEU A 738 " pdb=" CG LEU A 738 " ideal model delta sigma weight residual 116.30 133.58 -17.28 3.50e+00 8.16e-02 2.44e+01 angle pdb=" C3 NAG B 2 " pdb=" C4 NAG B 2 " pdb=" O4 NAG B 2 " ideal model delta sigma weight residual 110.01 119.21 -9.20 1.87e+00 2.86e-01 2.42e+01 ... (remaining 14732 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.36: 6227 32.36 - 64.72: 191 64.72 - 97.08: 11 97.08 - 129.43: 0 129.43 - 161.79: 2 Dihedral angle restraints: 6431 sinusoidal: 2605 harmonic: 3826 Sorted by residual: dihedral pdb=" CA ALA A1020 " pdb=" C ALA A1020 " pdb=" N PRO A1021 " pdb=" CA PRO A1021 " ideal model delta harmonic sigma weight residual 180.00 -120.56 -59.44 0 5.00e+00 4.00e-02 1.41e+02 dihedral pdb=" CA THR A 511 " pdb=" C THR A 511 " pdb=" N PRO A 512 " pdb=" CA PRO A 512 " ideal model delta harmonic sigma weight residual 180.00 128.89 51.11 0 5.00e+00 4.00e-02 1.04e+02 dihedral pdb=" CA LEU C 243 " pdb=" C LEU C 243 " pdb=" N ASP C 244 " pdb=" CA ASP C 244 " ideal model delta harmonic sigma weight residual 180.00 146.95 33.05 0 5.00e+00 4.00e-02 4.37e+01 ... (remaining 6428 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 1296 0.079 - 0.158: 339 0.158 - 0.237: 42 0.237 - 0.316: 4 0.316 - 0.395: 3 Chirality restraints: 1684 Sorted by residual: chirality pdb=" CB ILE A 219 " pdb=" CA ILE A 219 " pdb=" CG1 ILE A 219 " pdb=" CG2 ILE A 219 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.40 2.00e-01 2.50e+01 3.90e+00 chirality pdb=" C4 NAG B 2 " pdb=" C3 NAG B 2 " pdb=" C5 NAG B 2 " pdb=" O4 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.51 -2.13 -0.39 2.00e-01 2.50e+01 3.74e+00 chirality pdb=" CG LEU A 964 " pdb=" CB LEU A 964 " pdb=" CD1 LEU A 964 " pdb=" CD2 LEU A 964 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.74e+00 ... (remaining 1681 not shown) Planarity restraints: 1838 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " 0.351 2.00e-02 2.50e+03 3.00e-01 1.12e+03 pdb=" C7 NAG B 1 " -0.086 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " 0.166 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " -0.530 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " 0.099 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 402 " 0.270 2.00e-02 2.50e+03 2.29e-01 6.58e+02 pdb=" C7 NAG C 402 " -0.068 2.00e-02 2.50e+03 pdb=" C8 NAG C 402 " 0.173 2.00e-02 2.50e+03 pdb=" N2 NAG C 402 " -0.394 2.00e-02 2.50e+03 pdb=" O7 NAG C 402 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 401 " -0.230 2.00e-02 2.50e+03 1.95e-01 4.74e+02 pdb=" C7 NAG C 401 " 0.056 2.00e-02 2.50e+03 pdb=" C8 NAG C 401 " -0.156 2.00e-02 2.50e+03 pdb=" N2 NAG C 401 " 0.330 2.00e-02 2.50e+03 pdb=" O7 NAG C 401 " -0.001 2.00e-02 2.50e+03 ... (remaining 1835 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 479 2.71 - 3.26: 9969 3.26 - 3.80: 17504 3.80 - 4.35: 22761 4.35 - 4.90: 37955 Nonbonded interactions: 88668 Sorted by model distance: nonbonded pdb=" OD2 ASP A 409 " pdb="MG MG A1202 " model vdw 2.159 2.170 nonbonded pdb=" O TYR A 881 " pdb=" OG1 THR A 886 " model vdw 2.244 2.440 nonbonded pdb=" OH TYR C 134 " pdb=" OG SER C 177 " model vdw 2.245 2.440 nonbonded pdb=" O GLU A 222 " pdb=" OH TYR A 269 " model vdw 2.263 2.440 nonbonded pdb=" O CYS A 50 " pdb=" OG1 THR A 270 " model vdw 2.278 2.440 ... (remaining 88663 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 56 5.16 5 C 6863 2.51 5 N 1757 2.21 5 O 1922 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.630 Check model and map are aligned: 0.160 Convert atoms to be neutral: 0.090 Process input model: 30.660 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 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 : 0.013 0.125 10852 Z= 0.808 Angle : 1.227 17.279 14737 Z= 0.656 Chirality : 0.070 0.395 1684 Planarity : 0.014 0.300 1835 Dihedral : 15.258 161.793 3954 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.61 % Favored : 91.24 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.08 % 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: -3.98 (0.18), residues: 1301 helix: -2.61 (0.16), residues: 577 sheet: -1.21 (0.39), residues: 156 loop : -3.03 (0.21), residues: 568 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 127 time to evaluate : 1.244 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 129 average time/residue: 0.2504 time to fit residues: 45.6258 Evaluate side-chains 99 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 98 time to evaluate : 1.267 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0977 time to fit residues: 2.0380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 54 optimal weight: 20.0000 chunk 33 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 52 optimal weight: 0.5980 chunk 101 optimal weight: 0.5980 chunk 39 optimal weight: 30.0000 chunk 61 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 118 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 51 ASN A 78 ASN A 124 HIS A 128 ASN A 136 GLN ** A 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 GLN A 261 GLN A 381 HIS A 397 ASN ** A 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 679 ASN ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 10852 Z= 0.180 Angle : 0.650 9.060 14737 Z= 0.339 Chirality : 0.045 0.204 1684 Planarity : 0.006 0.084 1835 Dihedral : 8.824 162.756 1466 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.00 % Favored : 93.85 % Rotamer Outliers : 1.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 3.70 % 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: -2.66 (0.21), residues: 1301 helix: -1.13 (0.20), residues: 582 sheet: -1.05 (0.38), residues: 160 loop : -2.65 (0.23), residues: 559 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 104 time to evaluate : 1.289 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 10 residues processed: 119 average time/residue: 0.2412 time to fit residues: 40.8876 Evaluate side-chains 104 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 94 time to evaluate : 1.128 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1431 time to fit residues: 3.8615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 65 optimal weight: 8.9990 chunk 36 optimal weight: 3.9990 chunk 98 optimal weight: 0.4980 chunk 80 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 117 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 94 optimal weight: 0.0070 overall best weight: 1.4402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 453 GLN ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 HIS ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 10852 Z= 0.245 Angle : 0.634 8.793 14737 Z= 0.327 Chirality : 0.045 0.190 1684 Planarity : 0.005 0.085 1835 Dihedral : 8.341 157.730 1466 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.38 % Favored : 93.47 % Rotamer Outliers : 1.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.22), residues: 1301 helix: -0.57 (0.21), residues: 582 sheet: -0.95 (0.38), residues: 166 loop : -2.46 (0.23), residues: 553 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 109 time to evaluate : 1.191 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 12 residues processed: 129 average time/residue: 0.2328 time to fit residues: 42.9903 Evaluate side-chains 111 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 99 time to evaluate : 1.173 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0994 time to fit residues: 3.8350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 116 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 13 optimal weight: 7.9990 chunk 56 optimal weight: 9.9990 chunk 79 optimal weight: 0.5980 chunk 118 optimal weight: 4.9990 chunk 125 optimal weight: 0.7980 chunk 62 optimal weight: 0.0170 chunk 112 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 overall best weight: 0.8820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 10852 Z= 0.179 Angle : 0.583 7.915 14737 Z= 0.299 Chirality : 0.044 0.167 1684 Planarity : 0.005 0.083 1835 Dihedral : 7.914 153.969 1466 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.53 % Favored : 94.31 % Rotamer Outliers : 1.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.22), residues: 1301 helix: -0.14 (0.21), residues: 586 sheet: -0.89 (0.37), residues: 180 loop : -2.21 (0.25), residues: 535 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 101 time to evaluate : 1.247 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 8 residues processed: 119 average time/residue: 0.2163 time to fit residues: 38.0520 Evaluate side-chains 101 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 93 time to evaluate : 1.226 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1032 time to fit residues: 3.2469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 104 optimal weight: 0.0370 chunk 71 optimal weight: 3.9990 chunk 1 optimal weight: 20.0000 chunk 93 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 64 optimal weight: 10.0000 chunk 112 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 10852 Z= 0.234 Angle : 0.602 8.538 14737 Z= 0.307 Chirality : 0.044 0.174 1684 Planarity : 0.005 0.084 1835 Dihedral : 7.841 152.483 1466 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.07 % Favored : 93.77 % Rotamer Outliers : 0.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.23), residues: 1301 helix: 0.03 (0.22), residues: 575 sheet: -0.80 (0.38), residues: 180 loop : -2.06 (0.25), residues: 546 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 99 time to evaluate : 1.254 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 106 average time/residue: 0.2192 time to fit residues: 34.2137 Evaluate side-chains 99 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 94 time to evaluate : 1.095 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0980 time to fit residues: 2.5352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 42 optimal weight: 7.9990 chunk 113 optimal weight: 0.9980 chunk 24 optimal weight: 0.0030 chunk 73 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 104 optimal weight: 0.2980 chunk 58 optimal weight: 30.0000 chunk 10 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 66 optimal weight: 8.9990 overall best weight: 0.8592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 10852 Z= 0.175 Angle : 0.565 8.014 14737 Z= 0.289 Chirality : 0.043 0.175 1684 Planarity : 0.005 0.078 1835 Dihedral : 7.598 149.614 1466 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.69 % Favored : 94.24 % Rotamer Outliers : 0.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.23), residues: 1301 helix: 0.24 (0.22), residues: 574 sheet: -0.65 (0.39), residues: 176 loop : -1.94 (0.25), residues: 551 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 96 time to evaluate : 1.348 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 105 average time/residue: 0.2395 time to fit residues: 37.9137 Evaluate side-chains 97 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 91 time to evaluate : 1.204 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1277 time to fit residues: 3.4603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 121 optimal weight: 2.9990 chunk 14 optimal weight: 20.0000 chunk 71 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 125 optimal weight: 0.9980 chunk 78 optimal weight: 0.0370 chunk 76 optimal weight: 1.9990 chunk 57 optimal weight: 8.9990 chunk 77 optimal weight: 0.7980 overall best weight: 0.9260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 10852 Z= 0.182 Angle : 0.564 7.881 14737 Z= 0.287 Chirality : 0.043 0.169 1684 Planarity : 0.005 0.080 1835 Dihedral : 7.479 146.559 1466 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.69 % Favored : 94.24 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.23), residues: 1301 helix: 0.33 (0.22), residues: 575 sheet: -0.54 (0.39), residues: 176 loop : -1.90 (0.25), residues: 550 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 94 time to evaluate : 1.339 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 102 average time/residue: 0.2260 time to fit residues: 34.5958 Evaluate side-chains 93 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 89 time to evaluate : 1.309 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1028 time to fit residues: 2.5139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 50 optimal weight: 9.9990 chunk 74 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 24 optimal weight: 0.0040 chunk 79 optimal weight: 0.8980 chunk 85 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 98 optimal weight: 0.0170 chunk 113 optimal weight: 0.7980 chunk 120 optimal weight: 4.9990 overall best weight: 0.5432 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 10852 Z= 0.149 Angle : 0.550 7.682 14737 Z= 0.281 Chirality : 0.042 0.176 1684 Planarity : 0.005 0.077 1835 Dihedral : 7.249 139.964 1466 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.69 % Favored : 94.24 % Rotamer Outliers : 0.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.23), residues: 1301 helix: 0.42 (0.22), residues: 578 sheet: -0.49 (0.39), residues: 176 loop : -1.87 (0.25), residues: 547 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 92 time to evaluate : 1.397 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 95 average time/residue: 0.2219 time to fit residues: 32.3827 Evaluate side-chains 93 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 89 time to evaluate : 1.305 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1142 time to fit residues: 2.6798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 70 optimal weight: 0.3980 chunk 50 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 123 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 144 ASN ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 10852 Z= 0.213 Angle : 0.573 8.228 14737 Z= 0.292 Chirality : 0.043 0.169 1684 Planarity : 0.005 0.080 1835 Dihedral : 7.227 137.050 1466 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.53 % Favored : 94.31 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.23), residues: 1301 helix: 0.39 (0.22), residues: 571 sheet: -0.44 (0.39), residues: 176 loop : -1.77 (0.25), residues: 554 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 92 time to evaluate : 1.273 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 94 average time/residue: 0.2279 time to fit residues: 32.1267 Evaluate side-chains 88 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 1.233 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 75 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 chunk 85 optimal weight: 4.9990 chunk 129 optimal weight: 4.9990 chunk 119 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 chunk 10 optimal weight: 9.9990 chunk 79 optimal weight: 0.9980 chunk 63 optimal weight: 7.9990 chunk 81 optimal weight: 0.5980 chunk 109 optimal weight: 2.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 583 GLN ** A 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 10852 Z= 0.212 Angle : 0.574 8.136 14737 Z= 0.292 Chirality : 0.044 0.178 1684 Planarity : 0.005 0.080 1835 Dihedral : 7.157 133.995 1466 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.53 % Favored : 94.39 % Rotamer Outliers : 0.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.23), residues: 1301 helix: 0.39 (0.22), residues: 571 sheet: -0.60 (0.38), residues: 186 loop : -1.70 (0.26), residues: 544 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 86 time to evaluate : 1.197 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 89 average time/residue: 0.2191 time to fit residues: 29.5403 Evaluate side-chains 88 residues out of total 1151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 86 time to evaluate : 1.264 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1521 time to fit residues: 2.7105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 31 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 15 optimal weight: 0.2980 chunk 28 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 43 optimal weight: 20.0000 chunk 106 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 249 ASN ** 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 = 0.4036 r_free = 0.4036 target = 0.192069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.159384 restraints weight = 10296.591| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 1.17 r_work: 0.3393 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 10852 Z= 0.302 Angle : 0.634 9.687 14737 Z= 0.321 Chirality : 0.046 0.191 1684 Planarity : 0.005 0.083 1835 Dihedral : 7.301 132.568 1466 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.30 % Favored : 93.62 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 3.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.23), residues: 1301 helix: 0.23 (0.22), residues: 564 sheet: -0.61 (0.38), residues: 186 loop : -1.76 (0.26), residues: 551 =============================================================================== Job complete usr+sys time: 2058.27 seconds wall clock time: 38 minutes 20.32 seconds (2300.32 seconds total)