Starting phenix.real_space_refine on Mon Aug 25 10:44:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m6h_23696/08_2025/7m6h_23696_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m6h_23696/08_2025/7m6h_23696.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7m6h_23696/08_2025/7m6h_23696_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m6h_23696/08_2025/7m6h_23696_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7m6h_23696/08_2025/7m6h_23696.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m6h_23696/08_2025/7m6h_23696.map" } resolution = 4.0 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 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= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 127 5.16 5 C 17404 2.51 5 N 4534 2.21 5 O 5314 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27379 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 7823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7823 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 49, 'TRANS': 952} Chain breaks: 7 Chain: "B" Number of atoms: 7823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7823 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 49, 'TRANS': 952} Chain breaks: 7 Chain: "C" Number of atoms: 7823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 7823 Classifications: {'peptide': 1002} Link IDs: {'PTRANS': 49, 'TRANS': 952} Chain breaks: 7 Chain: "D" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 953 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain: "E" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 953 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain: "F" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 806 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 7, 'TRANS': 101} Chain: "G" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 806 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 7, 'TRANS': 101} Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 6.14, per 1000 atoms: 0.22 Number of scatterers: 27379 At special positions: 0 Unit cell: (134.695, 143.385, 191.18, 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 127 16.00 O 5314 8.00 N 4534 7.00 C 17404 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.02 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.02 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.02 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.04 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=1.45 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=1.99 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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=1, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 343 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A 717 " " NAG A1308 " - " ASN A 801 " " NAG A1309 " - " ASN A1074 " " NAG B1301 " - " ASN B 234 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B 709 " " NAG B1305 " - " ASN B 717 " " NAG B1306 " - " ASN B 801 " " NAG B1307 " - " ASN B1134 " " NAG B1308 " - " ASN B 331 " " NAG C1301 " - " ASN A 282 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 234 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 165 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C 717 " " NAG C1309 " - " ASN C 801 " " NAG C1310 " - " ASN C 331 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.09 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 1.4 microseconds 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6458 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 0 sheets defined 21.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.529A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 403 through 409 removed outlier: 3.581A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 747 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 782 Processing helix chain 'A' and resid 816 through 825 removed outlier: 3.560A pdb=" N LYS A 825 " --> pdb=" O LEU A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.902A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.378A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1031 removed outlier: 3.638A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.528A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 404 through 410 removed outlier: 4.191A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 739 through 744 Processing helix chain 'B' and resid 746 through 755 Processing helix chain 'B' and resid 758 through 782 Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.681A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.688A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.707A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 966 removed outlier: 4.124A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.297A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.102A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 366 through 371 Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.875A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 747 through 755 Processing helix chain 'C' and resid 758 through 782 Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.792A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.142A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 966 removed outlier: 4.127A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.245A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.640A pdb=" N ASP D 86 " --> pdb=" O ARG D 83 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N THR D 87 " --> pdb=" O SER D 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 83 through 87' Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.796A pdb=" N SER E 31 " --> pdb=" O THR E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 87 removed outlier: 3.815A pdb=" N ASP E 86 " --> pdb=" O ARG E 83 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR E 87 " --> pdb=" O SER E 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 83 through 87' Processing helix chain 'F' and resid 26 through 30 removed outlier: 4.088A pdb=" N ALA F 29 " --> pdb=" O SER F 27A" (cutoff:3.500A) 490 hydrogen bonds defined for protein. 1452 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: 3.29 Time building geometry restraints manager: 2.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 4474 1.31 - 1.44: 7794 1.44 - 1.57: 15557 1.57 - 1.70: 1 1.70 - 1.83: 161 Bond restraints: 27987 Sorted by residual: bond pdb=" C VAL A 320 " pdb=" N GLN A 321 " ideal model delta sigma weight residual 1.326 1.237 0.090 1.84e-02 2.95e+03 2.37e+01 bond pdb=" C ARG C 357 " pdb=" O ARG C 357 " ideal model delta sigma weight residual 1.234 1.175 0.059 1.26e-02 6.30e+03 2.19e+01 bond pdb=" N PRO D 112 " pdb=" CD PRO D 112 " ideal model delta sigma weight residual 1.473 1.522 -0.049 1.40e-02 5.10e+03 1.24e+01 bond pdb=" N PRO E 112 " pdb=" CD PRO E 112 " ideal model delta sigma weight residual 1.473 1.521 -0.048 1.40e-02 5.10e+03 1.19e+01 bond pdb=" N ILE C 402 " pdb=" CA ILE C 402 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.11e-02 8.12e+03 1.18e+01 ... (remaining 27982 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.31: 37699 4.31 - 8.63: 340 8.63 - 12.94: 32 12.94 - 17.26: 1 17.26 - 21.57: 1 Bond angle restraints: 38073 Sorted by residual: angle pdb=" CA PRO D 112 " pdb=" N PRO D 112 " pdb=" CD PRO D 112 " ideal model delta sigma weight residual 112.00 99.50 12.50 1.40e+00 5.10e-01 7.97e+01 angle pdb=" CA PRO E 112 " pdb=" N PRO E 112 " pdb=" CD PRO E 112 " ideal model delta sigma weight residual 112.00 99.58 12.42 1.40e+00 5.10e-01 7.87e+01 angle pdb=" N ILE E 75 " pdb=" CA ILE E 75 " pdb=" C ILE E 75 " ideal model delta sigma weight residual 113.20 105.05 8.15 9.60e-01 1.09e+00 7.20e+01 angle pdb=" N VAL A 826 " pdb=" CA VAL A 826 " pdb=" C VAL A 826 " ideal model delta sigma weight residual 112.29 105.56 6.73 9.40e-01 1.13e+00 5.13e+01 angle pdb=" C PRO G 15 " pdb=" CA PRO G 15 " pdb=" CB PRO G 15 " ideal model delta sigma weight residual 112.64 100.60 12.04 1.74e+00 3.30e-01 4.79e+01 ... (remaining 38068 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 15405 17.94 - 35.88: 1281 35.88 - 53.82: 215 53.82 - 71.76: 66 71.76 - 89.70: 24 Dihedral angle restraints: 16991 sinusoidal: 6930 harmonic: 10061 Sorted by residual: dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 177.32 -84.32 1 1.00e+01 1.00e-02 8.65e+01 dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 -161.65 75.65 1 1.00e+01 1.00e-02 7.22e+01 dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 92 " pdb=" CB CYS E 92 " ideal model delta sinusoidal sigma weight residual 93.00 168.07 -75.07 1 1.00e+01 1.00e-02 7.13e+01 ... (remaining 16988 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.158: 4268 0.158 - 0.317: 116 0.317 - 0.475: 9 0.475 - 0.634: 5 0.634 - 0.792: 2 Chirality restraints: 4400 Sorted by residual: chirality pdb=" C1 NAG C1301 " pdb=" ND2 ASN A 282 " pdb=" C2 NAG C1301 " pdb=" O5 NAG C1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.61 -0.79 2.00e-01 2.50e+01 1.57e+01 chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.66 -0.74 2.00e-01 2.50e+01 1.38e+01 chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 61 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.81 -0.59 2.00e-01 2.50e+01 8.82e+00 ... (remaining 4397 not shown) Planarity restraints: 4917 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1310 " 0.320 2.00e-02 2.50e+03 2.80e-01 9.77e+02 pdb=" C7 NAG C1310 " -0.069 2.00e-02 2.50e+03 pdb=" C8 NAG C1310 " 0.091 2.00e-02 2.50e+03 pdb=" N2 NAG C1310 " -0.500 2.00e-02 2.50e+03 pdb=" O7 NAG C1310 " 0.158 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 234 " -0.013 2.00e-02 2.50e+03 6.35e-02 5.03e+01 pdb=" CG ASN C 234 " 0.091 2.00e-02 2.50e+03 pdb=" OD1 ASN C 234 " -0.075 2.00e-02 2.50e+03 pdb=" ND2 ASN C 234 " 0.053 2.00e-02 2.50e+03 pdb=" C1 NAG C1303 " -0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 234 " -0.023 2.00e-02 2.50e+03 4.59e-02 2.11e+01 pdb=" CG ASN C 234 " 0.079 2.00e-02 2.50e+03 pdb=" OD1 ASN C 234 " -0.030 2.00e-02 2.50e+03 pdb=" ND2 ASN C 234 " -0.026 2.00e-02 2.50e+03 ... (remaining 4914 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1647 2.72 - 3.26: 27978 3.26 - 3.81: 46939 3.81 - 4.35: 56702 4.35 - 4.90: 91334 Nonbonded interactions: 224600 Sorted by model distance: nonbonded pdb=" O ASN A 125 " pdb=" O6 NAG A1302 " model vdw 2.170 3.040 nonbonded pdb=" O GLN A 804 " pdb=" OG SER A 816 " model vdw 2.188 3.040 nonbonded pdb=" OD1 ASN B 370 " pdb=" OG1 THR E 100B" model vdw 2.226 3.040 nonbonded pdb=" OH TYR A 756 " pdb=" OD1 ASP A 994 " model vdw 2.231 3.040 nonbonded pdb=" OE1 GLN G 6 " pdb=" OG1 THR G 103 " model vdw 2.241 3.040 ... (remaining 224595 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 27 through 1308) selection = chain 'B' selection = (chain 'C' and resid 27 through 1308) } ncs_group { reference = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.150 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: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 22.560 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 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 0.583 28058 Z= 0.382 Angle : 1.196 39.579 38240 Z= 0.656 Chirality : 0.071 0.792 4400 Planarity : 0.009 0.280 4890 Dihedral : 13.704 89.695 10404 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.05 % Favored : 92.87 % Rotamer: Outliers : 0.27 % Allowed : 1.03 % Favored : 98.70 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.57 (0.13), residues: 3420 helix: -1.66 (0.18), residues: 622 sheet: -1.41 (0.22), residues: 493 loop : -1.87 (0.12), residues: 2305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 905 TYR 0.043 0.003 TYR C 917 PHE 0.054 0.003 PHE A 201 TRP 0.035 0.003 TRP E 47 HIS 0.017 0.002 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00646 (27987) covalent geometry : angle 1.13004 (38073) SS BOND : bond 0.08922 ( 43) SS BOND : angle 4.95974 ( 86) hydrogen bonds : bond 0.11652 ( 490) hydrogen bonds : angle 8.83768 ( 1452) Misc. bond : bond 0.00075 ( 1) link_NAG-ASN : bond 0.01026 ( 27) link_NAG-ASN : angle 7.03004 ( 81) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 329 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 PHE cc_start: 0.5971 (m-10) cc_final: 0.5604 (m-80) REVERT: A 515 PHE cc_start: 0.8932 (m-80) cc_final: 0.8575 (m-80) REVERT: A 562 PHE cc_start: 0.8679 (t80) cc_final: 0.8276 (t80) REVERT: A 960 ASN cc_start: 0.8586 (t0) cc_final: 0.8375 (t0) REVERT: A 1095 PHE cc_start: 0.7622 (m-10) cc_final: 0.7274 (m-10) REVERT: B 864 LEU cc_start: 0.7323 (tt) cc_final: 0.6515 (mm) REVERT: B 976 VAL cc_start: 0.8844 (t) cc_final: 0.8284 (t) REVERT: C 271 GLN cc_start: 0.5800 (mm-40) cc_final: 0.5509 (mm-40) REVERT: C 336 CYS cc_start: 0.2353 (OUTLIER) cc_final: 0.1801 (t) REVERT: C 1031 GLU cc_start: 0.7272 (mt-10) cc_final: 0.7031 (mt-10) REVERT: E 51 MET cc_start: 0.5989 (tpt) cc_final: 0.5565 (tpt) REVERT: G 32 ASP cc_start: 0.4368 (m-30) cc_final: 0.3948 (t0) outliers start: 8 outliers final: 1 residues processed: 336 average time/residue: 0.1605 time to fit residues: 88.1773 Evaluate side-chains 226 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 224 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 358 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 0.6980 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 448 ASN A 506 GLN ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 HIS ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 GLN B 49 HIS ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS ** B 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN D 72 ASN D 105 GLN ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.104913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.079489 restraints weight = 140473.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.081234 restraints weight = 79098.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.082402 restraints weight = 52578.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.083099 restraints weight = 39428.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.083712 restraints weight = 32709.165| |-----------------------------------------------------------------------------| r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 28058 Z= 0.216 Angle : 0.756 11.935 38240 Z= 0.384 Chirality : 0.050 0.478 4400 Planarity : 0.005 0.062 4890 Dihedral : 8.397 59.748 4310 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 18.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 1.53 % Allowed : 9.28 % Favored : 89.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.31 (0.13), residues: 3420 helix: -1.10 (0.19), residues: 631 sheet: -1.31 (0.22), residues: 479 loop : -1.80 (0.12), residues: 2310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 357 TYR 0.019 0.002 TYR B1047 PHE 0.026 0.002 PHE C 338 TRP 0.014 0.002 TRP A1102 HIS 0.007 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00449 (27987) covalent geometry : angle 0.72494 (38073) SS BOND : bond 0.00457 ( 43) SS BOND : angle 1.72067 ( 86) hydrogen bonds : bond 0.08109 ( 490) hydrogen bonds : angle 7.72131 ( 1452) Misc. bond : bond 0.00067 ( 1) link_NAG-ASN : bond 0.00655 ( 27) link_NAG-ASN : angle 4.45719 ( 81) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 246 time to evaluate : 1.000 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: A 516 GLU cc_start: 0.7262 (pm20) cc_final: 0.7056 (pm20) REVERT: A 960 ASN cc_start: 0.8678 (t0) cc_final: 0.8432 (t0) REVERT: A 1095 PHE cc_start: 0.7853 (m-10) cc_final: 0.7578 (m-10) REVERT: B 201 PHE cc_start: 0.6774 (t80) cc_final: 0.6458 (t80) REVERT: B 402 ILE cc_start: 0.3613 (tp) cc_final: 0.3333 (tp) REVERT: C 40 ASP cc_start: 0.7208 (t0) cc_final: 0.7007 (t0) REVERT: C 229 LEU cc_start: 0.8791 (tp) cc_final: 0.8573 (mp) REVERT: C 336 CYS cc_start: 0.4273 (OUTLIER) cc_final: 0.3777 (t) REVERT: E 51 MET cc_start: 0.5955 (tpt) cc_final: 0.5643 (tpt) REVERT: E 69 MET cc_start: 0.3937 (mpp) cc_final: 0.3290 (mmp) REVERT: E 80 MET cc_start: 0.6963 (tpt) cc_final: 0.6561 (tpt) REVERT: G 32 ASP cc_start: 0.4246 (m-30) cc_final: 0.3800 (t0) REVERT: G 47 LEU cc_start: 0.8728 (mt) cc_final: 0.8424 (pp) outliers start: 46 outliers final: 27 residues processed: 276 average time/residue: 0.1395 time to fit residues: 65.0880 Evaluate side-chains 236 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 208 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1051 SER Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 730 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 777 ASN Chi-restraints excluded: chain B residue 800 PHE Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 497 PHE Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain E residue 100 TYR Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain G residue 97 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 186 optimal weight: 0.8980 chunk 294 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 58 optimal weight: 9.9990 chunk 143 optimal weight: 2.9990 chunk 231 optimal weight: 10.0000 chunk 172 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 150 optimal weight: 8.9990 chunk 236 optimal weight: 5.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN F 53 ASN ** G 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.101812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.076849 restraints weight = 126903.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.078898 restraints weight = 69214.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.080029 restraints weight = 44482.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.081041 restraints weight = 33338.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.081602 restraints weight = 26447.007| |-----------------------------------------------------------------------------| r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 28058 Z= 0.154 Angle : 0.678 12.260 38240 Z= 0.341 Chirality : 0.048 0.458 4400 Planarity : 0.005 0.058 4890 Dihedral : 7.670 58.664 4310 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 2.09 % Allowed : 12.90 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.24 (0.13), residues: 3420 helix: -0.88 (0.19), residues: 630 sheet: -1.29 (0.23), residues: 478 loop : -1.80 (0.12), residues: 2312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 237 TYR 0.022 0.001 TYR C 266 PHE 0.023 0.002 PHE C 898 TRP 0.011 0.001 TRP B 353 HIS 0.013 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00322 (27987) covalent geometry : angle 0.65045 (38073) SS BOND : bond 0.00684 ( 43) SS BOND : angle 1.50553 ( 86) hydrogen bonds : bond 0.07299 ( 490) hydrogen bonds : angle 7.44839 ( 1452) Misc. bond : bond 0.00050 ( 1) link_NAG-ASN : bond 0.00613 ( 27) link_NAG-ASN : angle 3.96016 ( 81) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 242 time to evaluate : 1.025 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: A 115 GLN cc_start: -0.1471 (OUTLIER) cc_final: -0.2357 (tt0) REVERT: A 316 SER cc_start: 0.8889 (t) cc_final: 0.8670 (p) REVERT: A 516 GLU cc_start: 0.7764 (pm20) cc_final: 0.7444 (pm20) REVERT: A 589 PRO cc_start: 0.6479 (Cg_exo) cc_final: 0.6248 (Cg_endo) REVERT: A 960 ASN cc_start: 0.8893 (t0) cc_final: 0.8668 (t0) REVERT: A 1037 SER cc_start: 0.8695 (t) cc_final: 0.8408 (m) REVERT: A 1095 PHE cc_start: 0.7917 (m-10) cc_final: 0.7551 (m-10) REVERT: B 402 ILE cc_start: 0.3950 (tp) cc_final: 0.3673 (tp) REVERT: B 697 MET cc_start: 0.7460 (ppp) cc_final: 0.7043 (ppp) REVERT: B 764 ASN cc_start: 0.8902 (t0) cc_final: 0.8520 (t0) REVERT: C 200 TYR cc_start: 0.7959 (m-80) cc_final: 0.7513 (m-80) REVERT: C 336 CYS cc_start: 0.2314 (OUTLIER) cc_final: 0.1830 (t) REVERT: C 360 ASN cc_start: 0.4639 (OUTLIER) cc_final: 0.3128 (t0) REVERT: G 32 ASP cc_start: 0.4302 (m-30) cc_final: 0.3823 (t0) outliers start: 63 outliers final: 34 residues processed: 290 average time/residue: 0.1485 time to fit residues: 72.6639 Evaluate side-chains 235 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 198 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 360 ASN Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 100 TYR Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain G residue 97 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 68 optimal weight: 2.9990 chunk 180 optimal weight: 4.9990 chunk 115 optimal weight: 9.9990 chunk 88 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 151 optimal weight: 4.9990 chunk 323 optimal weight: 10.0000 chunk 271 optimal weight: 0.3980 chunk 163 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 152 optimal weight: 5.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 787 GLN A 804 GLN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 ASN ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN C 360 ASN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN E 3 GLN ** G 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.101837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.077056 restraints weight = 125500.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.079050 restraints weight = 68587.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.080398 restraints weight = 44373.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.081281 restraints weight = 32264.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.081777 restraints weight = 25786.115| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28058 Z= 0.145 Angle : 0.657 11.560 38240 Z= 0.331 Chirality : 0.047 0.444 4400 Planarity : 0.004 0.054 4890 Dihedral : 7.390 58.639 4310 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 2.86 % Allowed : 14.76 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.13 (0.14), residues: 3420 helix: -0.87 (0.19), residues: 640 sheet: -1.22 (0.23), residues: 476 loop : -1.70 (0.12), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 44 TYR 0.016 0.001 TYR C 365 PHE 0.021 0.002 PHE A 392 TRP 0.012 0.001 TRP B 353 HIS 0.010 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00308 (27987) covalent geometry : angle 0.63273 (38073) SS BOND : bond 0.00472 ( 43) SS BOND : angle 1.46124 ( 86) hydrogen bonds : bond 0.06941 ( 490) hydrogen bonds : angle 7.24627 ( 1452) Misc. bond : bond 0.00045 ( 1) link_NAG-ASN : bond 0.00568 ( 27) link_NAG-ASN : angle 3.63987 ( 81) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 225 time to evaluate : 0.989 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: A 58 PHE cc_start: 0.7899 (m-10) cc_final: 0.6255 (m-10) REVERT: A 115 GLN cc_start: -0.1452 (OUTLIER) cc_final: -0.2345 (tt0) REVERT: A 201 PHE cc_start: 0.7763 (m-80) cc_final: 0.7526 (m-10) REVERT: A 275 PHE cc_start: 0.6245 (m-10) cc_final: 0.5928 (m-10) REVERT: A 316 SER cc_start: 0.8889 (t) cc_final: 0.8685 (p) REVERT: A 516 GLU cc_start: 0.7752 (pm20) cc_final: 0.7457 (pm20) REVERT: A 589 PRO cc_start: 0.6497 (Cg_exo) cc_final: 0.6289 (Cg_endo) REVERT: A 864 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8682 (mm) REVERT: A 950 ASP cc_start: 0.8255 (p0) cc_final: 0.7626 (p0) REVERT: A 1037 SER cc_start: 0.8720 (t) cc_final: 0.8381 (m) REVERT: A 1095 PHE cc_start: 0.7888 (m-10) cc_final: 0.7541 (m-10) REVERT: B 697 MET cc_start: 0.7334 (ppp) cc_final: 0.7023 (ppp) REVERT: B 764 ASN cc_start: 0.8875 (t0) cc_final: 0.8521 (t0) REVERT: B 873 TYR cc_start: 0.7570 (OUTLIER) cc_final: 0.7209 (t80) REVERT: C 200 TYR cc_start: 0.7987 (m-80) cc_final: 0.7520 (m-80) REVERT: C 336 CYS cc_start: 0.2020 (OUTLIER) cc_final: -0.0370 (t) REVERT: C 515 PHE cc_start: 0.0602 (OUTLIER) cc_final: 0.0081 (p90) REVERT: E 69 MET cc_start: 0.3500 (tpp) cc_final: 0.3229 (mmm) REVERT: F 75 ILE cc_start: -0.0364 (OUTLIER) cc_final: -0.0582 (mp) REVERT: G 32 ASP cc_start: 0.4121 (m-30) cc_final: 0.3632 (t0) REVERT: G 45 LYS cc_start: 0.8091 (mppt) cc_final: 0.7811 (mppt) REVERT: G 47 LEU cc_start: 0.8646 (mp) cc_final: 0.8356 (pp) outliers start: 86 outliers final: 43 residues processed: 296 average time/residue: 0.1401 time to fit residues: 69.9959 Evaluate side-chains 249 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 200 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 497 PHE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 100 TYR Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain G residue 97 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 253 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 126 optimal weight: 0.3980 chunk 217 optimal weight: 0.4980 chunk 160 optimal weight: 6.9990 chunk 67 optimal weight: 0.3980 chunk 301 optimal weight: 2.9990 chunk 262 optimal weight: 1.9990 chunk 330 optimal weight: 0.6980 chunk 280 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 ASN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN B 61 ASN ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN B 519 HIS ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B 965 GLN C 239 GLN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** C1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 GLN D 3 GLN ** G 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.106546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.081495 restraints weight = 138570.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.083295 restraints weight = 77144.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.084460 restraints weight = 50627.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 66)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.085271 restraints weight = 37890.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.085712 restraints weight = 31292.357| |-----------------------------------------------------------------------------| r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28058 Z= 0.127 Angle : 0.655 12.715 38240 Z= 0.328 Chirality : 0.047 0.435 4400 Planarity : 0.004 0.052 4890 Dihedral : 7.161 59.423 4310 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 2.43 % Allowed : 16.32 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.07 (0.14), residues: 3420 helix: -0.82 (0.19), residues: 642 sheet: -1.18 (0.24), residues: 475 loop : -1.66 (0.13), residues: 2303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 237 TYR 0.024 0.001 TYR C 365 PHE 0.032 0.002 PHE F 62 TRP 0.011 0.001 TRP B 353 HIS 0.008 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00271 (27987) covalent geometry : angle 0.63378 (38073) SS BOND : bond 0.00611 ( 43) SS BOND : angle 1.53201 ( 86) hydrogen bonds : bond 0.06539 ( 490) hydrogen bonds : angle 7.14698 ( 1452) Misc. bond : bond 0.00035 ( 1) link_NAG-ASN : bond 0.00581 ( 27) link_NAG-ASN : angle 3.38542 ( 81) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 239 time to evaluate : 0.818 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: A 115 GLN cc_start: -0.1557 (OUTLIER) cc_final: -0.2366 (tt0) REVERT: A 201 PHE cc_start: 0.7992 (m-80) cc_final: 0.7699 (m-10) REVERT: A 950 ASP cc_start: 0.8119 (p0) cc_final: 0.7714 (p0) REVERT: A 988 GLU cc_start: 0.8077 (mp0) cc_final: 0.7728 (mp0) REVERT: A 1037 SER cc_start: 0.8758 (t) cc_final: 0.8534 (m) REVERT: A 1095 PHE cc_start: 0.7809 (m-10) cc_final: 0.7475 (m-10) REVERT: B 364 ASP cc_start: 0.6978 (p0) cc_final: 0.6608 (t0) REVERT: B 697 MET cc_start: 0.7165 (ppp) cc_final: 0.6924 (ppp) REVERT: B 764 ASN cc_start: 0.8832 (t0) cc_final: 0.8409 (t0) REVERT: B 873 TYR cc_start: 0.7318 (OUTLIER) cc_final: 0.7067 (t80) REVERT: C 200 TYR cc_start: 0.8067 (m-80) cc_final: 0.7593 (m-80) REVERT: C 515 PHE cc_start: 0.0540 (OUTLIER) cc_final: 0.0158 (p90) REVERT: C 802 PHE cc_start: 0.8113 (m-10) cc_final: 0.7820 (m-80) REVERT: D 91 PHE cc_start: 0.5511 (OUTLIER) cc_final: 0.5236 (t80) REVERT: G 32 ASP cc_start: 0.3906 (m-30) cc_final: 0.3402 (t0) outliers start: 73 outliers final: 42 residues processed: 296 average time/residue: 0.1535 time to fit residues: 76.2687 Evaluate side-chains 254 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 208 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 1033 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 497 PHE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 91 PHE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 100 TYR Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain G residue 97 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 226 optimal weight: 20.0000 chunk 58 optimal weight: 5.9990 chunk 162 optimal weight: 0.7980 chunk 130 optimal weight: 6.9990 chunk 308 optimal weight: 20.0000 chunk 59 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 296 optimal weight: 0.0870 chunk 137 optimal weight: 0.9990 chunk 28 optimal weight: 0.0570 chunk 295 optimal weight: 8.9990 overall best weight: 0.5880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS C 239 GLN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 34 HIS ** G 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.102952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.078584 restraints weight = 124457.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.080572 restraints weight = 69230.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.081835 restraints weight = 44913.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.082611 restraints weight = 32849.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.083165 restraints weight = 26649.546| |-----------------------------------------------------------------------------| r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28058 Z= 0.126 Angle : 0.656 10.728 38240 Z= 0.328 Chirality : 0.047 0.421 4400 Planarity : 0.004 0.052 4890 Dihedral : 6.949 59.548 4309 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 2.86 % Allowed : 16.59 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.07 (0.14), residues: 3420 helix: -0.84 (0.19), residues: 640 sheet: -1.14 (0.24), residues: 495 loop : -1.66 (0.13), residues: 2285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 408 TYR 0.021 0.001 TYR C 365 PHE 0.020 0.001 PHE F 62 TRP 0.012 0.001 TRP B 353 HIS 0.007 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00269 (27987) covalent geometry : angle 0.63763 (38073) SS BOND : bond 0.00291 ( 43) SS BOND : angle 1.32065 ( 86) hydrogen bonds : bond 0.06284 ( 490) hydrogen bonds : angle 6.98895 ( 1452) Misc. bond : bond 0.00032 ( 1) link_NAG-ASN : bond 0.00556 ( 27) link_NAG-ASN : angle 3.21083 ( 81) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6840 Ramachandran restraints generated. 3420 Oldfield, 0 Emsley, 3420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 243 time to evaluate : 0.993 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: A 115 GLN cc_start: -0.1428 (OUTLIER) cc_final: -0.2305 (tt0) REVERT: A 201 PHE cc_start: 0.7538 (m-80) cc_final: 0.7283 (m-10) REVERT: A 516 GLU cc_start: 0.7779 (pm20) cc_final: 0.6451 (pm20) REVERT: A 756 TYR cc_start: 0.7210 (m-10) cc_final: 0.6870 (m-10) REVERT: A 1037 SER cc_start: 0.8730 (t) cc_final: 0.8507 (m) REVERT: A 1095 PHE cc_start: 0.7709 (m-10) cc_final: 0.7473 (m-10) REVERT: A 1125 ASN cc_start: 0.7829 (p0) cc_final: 0.7236 (t0) REVERT: B 364 ASP cc_start: 0.6771 (p0) cc_final: 0.6455 (t0) REVERT: B 764 ASN cc_start: 0.8706 (t0) cc_final: 0.8291 (t0) REVERT: B 873 TYR cc_start: 0.7231 (OUTLIER) cc_final: 0.6965 (t80) REVERT: B 1050 MET cc_start: 0.6837 (ptt) cc_final: 0.5946 (ptt) REVERT: C 200 TYR cc_start: 0.7947 (m-80) cc_final: 0.7478 (m-80) REVERT: C 515 PHE cc_start: 0.0186 (OUTLIER) cc_final: -0.0159 (p90) REVERT: C 802 PHE cc_start: 0.8027 (m-10) cc_final: 0.7806 (m-80) REVERT: D 91 PHE cc_start: 0.5763 (OUTLIER) cc_final: 0.5476 (t80) REVERT: E 69 MET cc_start: 0.0982 (tpp) cc_final: -0.1124 (tpp) REVERT: E 100 MET cc_start: 0.8220 (tpt) cc_final: 0.7959 (tpt) REVERT: G 32 ASP cc_start: 0.3803 (m-30) cc_final: 0.3428 (t0) REVERT: G 36 TYR cc_start: 0.6527 (OUTLIER) cc_final: 0.5285 (m-80) outliers start: 86 outliers final: 56 residues processed: 311 average time/residue: 0.1544 time to fit residues: 80.5414 Evaluate side-chains 272 residues out of total 3008 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 211 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 870 ILE Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1139 ASP Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 497 PHE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 774 GLN Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 873 TYR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 91 PHE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 100 TYR Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 110 THR Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain G residue 36 TYR Chi-restraints excluded: chain G residue 97 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.0051 > 50: distance: 54 - 59: 9.462 distance: 59 - 60: 8.084 distance: 60 - 61: 10.627 distance: 60 - 63: 11.978 distance: 61 - 62: 23.328 distance: 61 - 70: 11.472 distance: 63 - 64: 5.956 distance: 64 - 65: 10.996 distance: 64 - 66: 11.915 distance: 65 - 67: 3.673 distance: 66 - 68: 8.251 distance: 67 - 69: 7.345 distance: 68 - 69: 11.565 distance: 71 - 72: 7.863 distance: 71 - 74: 5.383 distance: 72 - 73: 14.169 distance: 72 - 78: 23.119 distance: 74 - 75: 17.341 distance: 75 - 76: 7.727 distance: 75 - 77: 7.200 distance: 78 - 79: 22.391 distance: 79 - 80: 33.397 distance: 80 - 81: 15.518 distance: 80 - 82: 17.830 distance: 82 - 83: 24.246 distance: 83 - 84: 9.375 distance: 83 - 86: 23.759 distance: 84 - 85: 22.821 distance: 84 - 90: 6.248 distance: 86 - 87: 40.157 distance: 87 - 88: 25.509 distance: 87 - 89: 18.133 distance: 90 - 91: 17.302 distance: 91 - 92: 10.033 distance: 91 - 94: 9.715 distance: 92 - 93: 18.655 distance: 92 - 97: 11.831 distance: 94 - 96: 8.936 distance: 97 - 98: 3.917 distance: 98 - 99: 36.610 distance: 98 - 101: 13.580 distance: 99 - 100: 36.458 distance: 99 - 104: 17.578 distance: 101 - 102: 19.361 distance: 101 - 103: 26.405 distance: 104 - 105: 16.387 distance: 105 - 106: 9.271 distance: 105 - 108: 37.107 distance: 106 - 107: 5.513 distance: 106 - 112: 17.155 distance: 108 - 109: 27.056 distance: 109 - 110: 30.155 distance: 109 - 111: 10.962 distance: 112 - 113: 30.354 distance: 112 - 118: 16.935 distance: 113 - 114: 24.824 distance: 113 - 116: 16.086 distance: 114 - 115: 6.534 distance: 114 - 119: 22.014 distance: 116 - 117: 18.327 distance: 117 - 118: 26.259 distance: 119 - 120: 11.506 distance: 119 - 125: 16.631 distance: 120 - 121: 15.903 distance: 120 - 123: 11.937 distance: 121 - 122: 15.778 distance: 121 - 126: 15.789 distance: 123 - 124: 22.923 distance: 124 - 125: 11.819 distance: 126 - 127: 5.216 distance: 127 - 128: 3.116 distance: 127 - 130: 14.411 distance: 128 - 129: 9.201 distance: 128 - 134: 8.659 distance: 130 - 131: 6.862 distance: 131 - 132: 21.454 distance: 131 - 133: 19.539