Starting phenix.real_space_refine on Sun Sep 13 06:44:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rod_54115/09_2026/9rod_54115_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rod_54115/09_2026/9rod_54115.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9rod_54115/09_2026/9rod_54115.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rod_54115/09_2026/9rod_54115.map" model { file = "/net/cci-nas-00/data/ceres_data/9rod_54115/09_2026/9rod_54115_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rod_54115/09_2026/9rod_54115_trim.cif" } resolution = 3.12 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= -0.000 sd= 0.020 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: 7 Type Number sf(0) Gaussians P 1 5.49 5 S 61 5.16 5 Na 3 4.78 5 C 6621 2.51 5 N 1702 2.21 5 O 1942 1.98 5 H 10155 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20485 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 15210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 984, 15210 Classifications: {'peptide': 984} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 41, 'TRANS': 942} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PHD:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 4575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 4575 Classifications: {'peptide': 282} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 261} Chain: "C" Number of atoms: 543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 543 Classifications: {'peptide': 34} Link IDs: {'PTRANS': 1, 'TRANS': 32} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 87 Unusual residues: {' NA': 3, 'CLR': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.55, per 1000 atoms: 0.17 Number of scatterers: 20485 At special positions: 0 Unit cell: (95.6494, 81.9852, 185.088, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 61 16.00 P 1 15.00 Na 3 11.00 O 1942 8.00 N 1702 7.00 C 6621 6.00 H 10155 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 175 " distance=2.03 Simple disulfide: pdb=" SG CYS B 213 " - pdb=" SG CYS B 276 " 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=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG B 401 " - " ASN B 193 " " NAG D 1 " - " ASN B 265 " " NAG E 1 " - " ASN B 158 " Time building additional restraints: 2.07 Conformation dependent library (CDL) restraints added in 620.9 milliseconds 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2396 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 9 sheets defined 50.4% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 37 through 45 Processing helix chain 'A' and resid 54 through 66 Processing helix chain 'A' and resid 80 through 87 removed outlier: 3.887A pdb=" N ARG A 84 " --> pdb=" O VAL A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 112 Processing helix chain 'A' and resid 117 through 149 removed outlier: 3.567A pdb=" N ILE A 147 " --> pdb=" O LYS A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 265 Processing helix chain 'A' and resid 272 through 303 Processing helix chain 'A' and resid 306 through 321 Processing helix chain 'A' and resid 325 through 344 Processing helix chain 'A' and resid 350 through 359 removed outlier: 3.880A pdb=" N VAL A 354 " --> pdb=" O ASN A 350 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLU A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N THR A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 371 Processing helix chain 'A' and resid 405 through 419 Processing helix chain 'A' and resid 431 through 435 Processing helix chain 'A' and resid 440 through 455 Processing helix chain 'A' and resid 457 through 463 Processing helix chain 'A' and resid 500 through 507 Processing helix chain 'A' and resid 521 through 538 Processing helix chain 'A' and resid 587 through 599 removed outlier: 4.422A pdb=" N ASP A 591 " --> pdb=" O ALA A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 622 Processing helix chain 'A' and resid 630 through 639 Processing helix chain 'A' and resid 641 through 645 Processing helix chain 'A' and resid 646 through 650 Processing helix chain 'A' and resid 664 through 675 Processing helix chain 'A' and resid 684 through 698 removed outlier: 3.700A pdb=" N GLN A 698 " --> pdb=" O GLY A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 710 No H-bonds generated for 'chain 'A' and resid 708 through 710' Processing helix chain 'A' and resid 711 through 718 Processing helix chain 'A' and resid 729 through 735 Processing helix chain 'A' and resid 745 through 772 removed outlier: 4.176A pdb=" N VAL A 749 " --> pdb=" O PHE A 745 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR A 771 " --> pdb=" O ALA A 767 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N SER A 772 " --> pdb=" O TYR A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 786 Proline residue: A 779 - end of helix Processing helix chain 'A' and resid 793 through 805 Processing helix chain 'A' and resid 806 through 814 removed outlier: 4.056A pdb=" N ALA A 813 " --> pdb=" O ALA A 809 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N TYR A 814 " --> pdb=" O ILE A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 824 Processing helix chain 'A' and resid 836 through 845 Processing helix chain 'A' and resid 846 through 867 removed outlier: 3.588A pdb=" N ILE A 850 " --> pdb=" O GLN A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 874 removed outlier: 4.238A pdb=" N VAL A 874 " --> pdb=" O GLY A 871 " (cutoff:3.500A) Processing helix chain 'A' and resid 876 through 882 Processing helix chain 'A' and resid 897 through 927 removed outlier: 3.929A pdb=" N ALA A 922 " --> pdb=" O VAL A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 938 Processing helix chain 'A' and resid 941 through 961 Processing helix chain 'A' and resid 963 through 968 Processing helix chain 'A' and resid 974 through 980 Processing helix chain 'A' and resid 981 through 1002 Processing helix chain 'A' and resid 1005 through 1012 Processing helix chain 'B' and resid 28 through 61 Processing helix chain 'B' and resid 94 through 97 Processing helix chain 'B' and resid 98 through 111 removed outlier: 4.540A pdb=" N LYS B 111 " --> pdb=" O ARG B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 118 removed outlier: 5.740A pdb=" N SER B 115 " --> pdb=" O TYR B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 157 Processing helix chain 'B' and resid 204 through 206 No H-bonds generated for 'chain 'B' and resid 204 through 206' Processing helix chain 'B' and resid 241 through 243 No H-bonds generated for 'chain 'B' and resid 241 through 243' Processing helix chain 'C' and resid 32 through 58 removed outlier: 3.917A pdb=" N ARG C 58 " --> pdb=" O ILE C 54 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 166 through 171 removed outlier: 5.115A pdb=" N LEU A 160 " --> pdb=" O GLU A 182 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU A 182 " --> pdb=" O LEU A 160 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU A 180 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N CYS A 239 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N LYS A 202 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N GLU A 241 " --> pdb=" O GLY A 200 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N GLY A 200 " --> pdb=" O GLU A 241 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N THR A 243 " --> pdb=" O ALA A 198 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ALA A 198 " --> pdb=" O THR A 243 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ARG A 245 " --> pdb=" O ILE A 196 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ASP A 192 " --> pdb=" O VAL A 249 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 187 through 188 removed outlier: 4.847A pdb=" N CYS A 239 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N LYS A 202 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N GLU A 241 " --> pdb=" O GLY A 200 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N GLY A 200 " --> pdb=" O GLU A 241 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N THR A 243 " --> pdb=" O ALA A 198 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ALA A 198 " --> pdb=" O THR A 243 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ARG A 245 " --> pdb=" O ILE A 196 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ASP A 192 " --> pdb=" O VAL A 249 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 346 through 348 removed outlier: 6.891A pdb=" N VAL A 702 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N VAL A 722 " --> pdb=" O VAL A 702 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N VAL A 704 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N MET A 724 " --> pdb=" O VAL A 704 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N GLY A 706 " --> pdb=" O MET A 724 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL A 603 " --> pdb=" O ILE A 678 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N PHE A 680 " --> pdb=" O VAL A 603 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N MET A 605 " --> pdb=" O PHE A 680 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 386 through 389 removed outlier: 7.393A pdb=" N SER A 580 " --> pdb=" O ALA A 379 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N MET A 381 " --> pdb=" O LEU A 578 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N LEU A 578 " --> pdb=" O MET A 381 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N PHE A 383 " --> pdb=" O VAL A 576 " (cutoff:3.500A) removed outlier: 9.758A pdb=" N VAL A 576 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 8.579A pdb=" N LEU A 573 " --> pdb=" O TYR A 549 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N TYR A 549 " --> pdb=" O LEU A 573 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N PHE A 575 " --> pdb=" O HIS A 547 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N HIS A 547 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY A 577 " --> pdb=" O PHE A 545 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N GLU A 484 " --> pdb=" O LYS A 466 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LYS A 466 " --> pdb=" O GLU A 484 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 386 through 389 removed outlier: 7.393A pdb=" N SER A 580 " --> pdb=" O ALA A 379 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N MET A 381 " --> pdb=" O LEU A 578 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N LEU A 578 " --> pdb=" O MET A 381 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N PHE A 383 " --> pdb=" O VAL A 576 " (cutoff:3.500A) removed outlier: 9.758A pdb=" N VAL A 576 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LEU A 573 " --> pdb=" O CYS A 508 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N GLY A 577 " --> pdb=" O LEU A 512 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 888 through 889 Processing sheet with id=AA7, first strand: chain 'B' and resid 77 through 79 Processing sheet with id=AA8, first strand: chain 'B' and resid 87 through 90 removed outlier: 6.332A pdb=" N ILE B 88 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 237 through 239 547 hydrogen bonds defined for protein. 1530 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.87 Time building geometry restraints manager: 2.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10129 1.03 - 1.23: 40 1.23 - 1.42: 4262 1.42 - 1.62: 6178 1.62 - 1.81: 91 Bond restraints: 20700 Sorted by residual: bond pdb=" OD1 PHD A 366 " pdb=" P PHD A 366 " ideal model delta sigma weight residual 1.816 1.778 0.038 2.00e-02 2.50e+03 3.54e+00 bond pdb=" C PHD A 366 " pdb=" O PHD A 366 " ideal model delta sigma weight residual 1.231 1.266 -0.035 2.00e-02 2.50e+03 3.03e+00 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.82e+00 bond pdb=" CG PHD A 366 " pdb=" OD2 PHD A 366 " ideal model delta sigma weight residual 1.218 1.250 -0.032 2.00e-02 2.50e+03 2.49e+00 bond pdb=" N PHD A 366 " pdb=" H PHD A 366 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.20e+00 ... (remaining 20695 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 37156 1.86 - 3.71: 254 3.71 - 5.57: 25 5.57 - 7.42: 3 7.42 - 9.28: 3 Bond angle restraints: 37441 Sorted by residual: angle pdb=" CG PHD A 366 " pdb=" OD1 PHD A 366 " pdb=" P PHD A 366 " ideal model delta sigma weight residual 125.58 116.30 9.28 3.00e+00 1.11e-01 9.57e+00 angle pdb=" OD1 PHD A 366 " pdb=" CG PHD A 366 " pdb=" OD2 PHD A 366 " ideal model delta sigma weight residual 126.03 117.49 8.54 3.00e+00 1.11e-01 8.10e+00 angle pdb=" CB MET A 381 " pdb=" CG MET A 381 " pdb=" SD MET A 381 " ideal model delta sigma weight residual 112.70 120.99 -8.29 3.00e+00 1.11e-01 7.64e+00 angle pdb=" OD1 PHD A 366 " pdb=" P PHD A 366 " pdb=" OP2 PHD A 366 " ideal model delta sigma weight residual 103.47 96.50 6.97 3.00e+00 1.11e-01 5.39e+00 angle pdb=" OD1 PHD A 366 " pdb=" P PHD A 366 " pdb=" OP1 PHD A 366 " ideal model delta sigma weight residual 97.64 104.60 -6.96 3.00e+00 1.11e-01 5.38e+00 ... (remaining 37436 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.42: 9191 23.42 - 46.85: 567 46.85 - 70.27: 173 70.27 - 93.69: 19 93.69 - 117.11: 3 Dihedral angle restraints: 9953 sinusoidal: 5601 harmonic: 4352 Sorted by residual: dihedral pdb=" C1 CLR A1101 " pdb=" C2 CLR A1101 " pdb=" C3 CLR A1101 " pdb=" C4 CLR A1101 " ideal model delta sinusoidal sigma weight residual 57.41 -59.70 117.11 1 3.00e+01 1.11e-03 1.55e+01 dihedral pdb=" CA GLY B 225 " pdb=" C GLY B 225 " pdb=" N ASN B 226 " pdb=" CA ASN B 226 " ideal model delta harmonic sigma weight residual 180.00 160.33 19.67 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" C1 CLR A1101 " pdb=" C2 CLR A1101 " pdb=" C3 CLR A1101 " pdb=" O1 CLR A1101 " ideal model delta sinusoidal sigma weight residual 180.04 64.05 115.99 1 3.00e+01 1.11e-03 1.53e+01 ... (remaining 9950 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1002 0.029 - 0.058: 430 0.058 - 0.087: 114 0.087 - 0.115: 73 0.115 - 0.144: 21 Chirality restraints: 1640 Sorted by residual: chirality pdb=" CA ILE B 176 " pdb=" N ILE B 176 " pdb=" C ILE B 176 " pdb=" CB ILE B 176 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.20e-01 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN B 158 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 4.64e-01 chirality pdb=" CA ILE A 430 " pdb=" N ILE A 430 " pdb=" C ILE A 430 " pdb=" CB ILE A 430 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.61e-01 ... (remaining 1637 not shown) Planarity restraints: 3058 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A 779 " -0.006 2.00e-02 2.50e+03 1.14e-02 1.30e+00 pdb=" C PRO A 779 " 0.020 2.00e-02 2.50e+03 pdb=" O PRO A 779 " -0.007 2.00e-02 2.50e+03 pdb=" N PHE A 780 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 365 " 0.006 2.00e-02 2.50e+03 1.09e-02 1.18e+00 pdb=" N PHD A 366 " -0.019 2.00e-02 2.50e+03 pdb=" CA PHD A 366 " 0.005 2.00e-02 2.50e+03 pdb=" H PHD A 366 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 859 " -0.011 2.00e-02 2.50e+03 5.81e-03 1.01e+00 pdb=" CG TYR A 859 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR A 859 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR A 859 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 859 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 859 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 859 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 859 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 TYR A 859 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 TYR A 859 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 TYR A 859 " 0.000 2.00e-02 2.50e+03 pdb=" HE2 TYR A 859 " -0.000 2.00e-02 2.50e+03 ... (remaining 3055 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.09: 410 2.09 - 2.72: 35054 2.72 - 3.34: 62017 3.34 - 3.97: 76389 3.97 - 4.60: 119908 Nonbonded interactions: 293778 Sorted by model distance: nonbonded pdb=" OE1 GLU A 632 " pdb=" H GLU A 632 " model vdw 1.458 2.450 nonbonded pdb=" OE1 GLU B 87 " pdb=" H GLU B 87 " model vdw 1.533 2.450 nonbonded pdb=" O GLY A 657 " pdb="HE22 GLN A 687 " model vdw 1.577 2.450 nonbonded pdb=" OE1 GLU B 165 " pdb=" H GLU B 165 " model vdw 1.581 2.450 nonbonded pdb=" HH TYR B 112 " pdb=" O GLN B 256 " model vdw 1.606 2.450 ... (remaining 293773 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 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 0.540 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: 0.140 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.640 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 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 : 0.003 0.038 10553 Z= 0.153 Angle : 0.548 9.278 14332 Z= 0.270 Chirality : 0.040 0.144 1640 Planarity : 0.003 0.024 1823 Dihedral : 15.985 117.113 4147 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.54 % Allowed : 16.61 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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 are not related in a simple way. whole: 0.56 (0.25), residues: 1291 helix: 1.76 (0.22), residues: 600 sheet: -0.86 (0.46), residues: 126 loop : -0.85 (0.27), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 64 TYR 0.017 0.001 TYR A 859 PHE 0.012 0.001 PHE B 24 TRP 0.012 0.001 TRP A 79 HIS 0.002 0.000 HIS A 483 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (10545) covalent geometry : angle 0.54659 / 0.27 (14311) SS BOND : bond 0.00091 / 0.03 ( 3) SS BOND : angle 0.55730 / 0.35 ( 6) hydrogen bonds : bond 0.14268 / 9.41 ( 536) hydrogen bonds : angle 5.86736 / 4.31 ( 1530) link_BETA1-4 : bond 0.00248 / 0.12 ( 2) link_BETA1-4 : angle 1.45495 / 0.87 ( 6) link_NAG-ASN : bond 0.00086 / 0.03 ( 3) link_NAG-ASN : angle 1.28347 / 0.73 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.466 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 outliers start: 6 outliers final: 5 residues processed: 95 average time/residue: 0.2496 time to fit residues: 33.5294 Evaluate side-chains 93 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 88 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain B residue 158 ASN Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain C residue 55 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 483 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.123566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.079815 restraints weight = 63474.780| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 3.34 r_work: 0.3062 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.0515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10553 Z= 0.156 Angle : 0.540 7.883 14332 Z= 0.278 Chirality : 0.040 0.168 1640 Planarity : 0.003 0.032 1823 Dihedral : 6.583 67.848 1710 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 1.26 % Allowed : 15.98 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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 are not related in a simple way. whole: 0.45 (0.24), residues: 1291 helix: 1.70 (0.22), residues: 610 sheet: -1.03 (0.45), residues: 125 loop : -0.97 (0.27), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 901 TYR 0.013 0.001 TYR A 859 PHE 0.015 0.001 PHE A 783 TRP 0.004 0.001 TRP A 977 HIS 0.002 0.001 HIS A 483 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.16 (10545) covalent geometry : angle 0.53900 / 0.28 (14311) SS BOND : bond 0.00197 / 0.07 ( 3) SS BOND : angle 0.53980 / 0.34 ( 6) hydrogen bonds : bond 0.04221 / 2.82 ( 536) hydrogen bonds : angle 4.94477 / 3.61 ( 1530) link_BETA1-4 : bond 0.00604 / 0.30 ( 2) link_BETA1-4 : angle 1.22221 / 0.68 ( 6) link_NAG-ASN : bond 0.00190 / 0.09 ( 3) link_NAG-ASN : angle 1.30514 / 0.61 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.472 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: symmetry clash outliers start: 14 outliers final: 12 residues processed: 105 average time/residue: 0.2141 time to fit residues: 32.1956 Evaluate side-chains 101 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 TRP Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 858 SER Chi-restraints excluded: chain A residue 965 ASP Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 158 ASN Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain C residue 55 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 12 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 61 optimal weight: 9.9990 chunk 116 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 127 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 chunk 20 optimal weight: 10.0000 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.123742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.079999 restraints weight = 63688.140| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 3.34 r_work: 0.3017 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.0718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10553 Z= 0.142 Angle : 0.521 6.008 14332 Z= 0.266 Chirality : 0.040 0.158 1640 Planarity : 0.003 0.033 1823 Dihedral : 5.750 67.728 1710 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 1.35 % Allowed : 15.62 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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 are not related in a simple way. whole: 0.46 (0.24), residues: 1291 helix: 1.68 (0.21), residues: 611 sheet: -0.88 (0.46), residues: 122 loop : -0.97 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 901 TYR 0.013 0.001 TYR A 859 PHE 0.012 0.001 PHE A 783 TRP 0.004 0.001 TRP A 977 HIS 0.002 0.000 HIS A 483 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (10545) covalent geometry : angle 0.51941 / 0.27 (14311) SS BOND : bond 0.00148 / 0.05 ( 3) SS BOND : angle 0.47258 / 0.30 ( 6) hydrogen bonds : bond 0.03730 / 2.49 ( 536) hydrogen bonds : angle 4.69396 / 3.43 ( 1530) link_BETA1-4 : bond 0.00328 / 0.16 ( 2) link_BETA1-4 : angle 1.08978 / 0.59 ( 6) link_NAG-ASN : bond 0.00086 / 0.04 ( 3) link_NAG-ASN : angle 1.33855 / 0.62 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.559 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 PHE cc_start: 0.4123 (OUTLIER) cc_final: 0.3313 (p90) REVERT: A 368 THR cc_start: 0.8529 (m) cc_final: 0.8245 (p) outliers start: 15 outliers final: 12 residues processed: 104 average time/residue: 0.2571 time to fit residues: 38.2627 Evaluate side-chains 105 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 TRP Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 858 SER Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 158 ASN Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain C residue 55 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 112 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 31 optimal weight: 0.4980 chunk 44 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 374 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.124876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.081127 restraints weight = 63728.978| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 3.37 r_work: 0.3046 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.0898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10553 Z= 0.101 Angle : 0.500 5.856 14332 Z= 0.254 Chirality : 0.039 0.159 1640 Planarity : 0.003 0.033 1823 Dihedral : 5.541 66.507 1710 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.17 % Allowed : 16.16 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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 are not related in a simple way. whole: 0.61 (0.24), residues: 1291 helix: 1.90 (0.22), residues: 599 sheet: -0.88 (0.46), residues: 122 loop : -0.94 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 503 TYR 0.010 0.001 TYR A 984 PHE 0.011 0.001 PHE A 783 TRP 0.004 0.001 TRP A 95 HIS 0.001 0.000 HIS A 610 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (10545) covalent geometry : angle 0.49832 / 0.25 (14311) SS BOND : bond 0.00089 / 0.03 ( 3) SS BOND : angle 0.45924 / 0.30 ( 6) hydrogen bonds : bond 0.03316 / 2.21 ( 536) hydrogen bonds : angle 4.45699 / 3.26 ( 1530) link_BETA1-4 : bond 0.00280 / 0.14 ( 2) link_BETA1-4 : angle 1.13385 / 0.62 ( 6) link_NAG-ASN : bond 0.00081 / 0.04 ( 3) link_NAG-ASN : angle 1.24717 / 0.59 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.652 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 THR cc_start: 0.8488 (m) cc_final: 0.8274 (p) REVERT: B 179 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8689 (ptmm) outliers start: 13 outliers final: 9 residues processed: 109 average time/residue: 0.2407 time to fit residues: 37.5750 Evaluate side-chains 105 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 TRP Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 158 ASN Chi-restraints excluded: chain B residue 179 LYS Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain C residue 55 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 119 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 51 optimal weight: 20.0000 chunk 83 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 46 optimal weight: 30.0000 chunk 27 optimal weight: 1.9990 chunk 39 optimal weight: 20.0000 chunk 67 optimal weight: 4.9990 chunk 19 optimal weight: 9.9990 chunk 48 optimal weight: 0.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.123472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.079650 restraints weight = 63750.074| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 3.35 r_work: 0.3019 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.0973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10553 Z= 0.184 Angle : 0.526 6.038 14332 Z= 0.270 Chirality : 0.040 0.161 1640 Planarity : 0.003 0.033 1823 Dihedral : 5.559 66.621 1710 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 1.71 % Allowed : 16.52 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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 are not related in a simple way. whole: 0.54 (0.24), residues: 1291 helix: 1.88 (0.22), residues: 599 sheet: -1.10 (0.45), residues: 125 loop : -0.97 (0.27), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 503 TYR 0.012 0.001 TYR A 859 PHE 0.012 0.001 PHE A 783 TRP 0.004 0.001 TRP A 79 HIS 0.001 0.000 HIS A 483 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 (10545) covalent geometry : angle 0.52509 / 0.27 (14311) SS BOND : bond 0.00202 / 0.07 ( 3) SS BOND : angle 0.47317 / 0.30 ( 6) hydrogen bonds : bond 0.03383 / 2.24 ( 536) hydrogen bonds : angle 4.51299 / 3.32 ( 1530) link_BETA1-4 : bond 0.00230 / 0.11 ( 2) link_BETA1-4 : angle 1.08452 / 0.59 ( 6) link_NAG-ASN : bond 0.00174 / 0.07 ( 3) link_NAG-ASN : angle 1.40449 / 0.64 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.565 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 16 residues processed: 109 average time/residue: 0.2420 time to fit residues: 37.8178 Evaluate side-chains 107 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 TRP Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 858 SER Chi-restraints excluded: chain A residue 959 SER Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 158 ASN Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain C residue 55 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 127 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 chunk 103 optimal weight: 0.0270 chunk 37 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 36 optimal weight: 8.9990 chunk 6 optimal weight: 4.9990 chunk 104 optimal weight: 0.3980 chunk 80 optimal weight: 0.7980 overall best weight: 1.0442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 374 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.124579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.080680 restraints weight = 63427.339| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 3.38 r_work: 0.3027 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10553 Z= 0.112 Angle : 0.500 5.909 14332 Z= 0.255 Chirality : 0.039 0.157 1640 Planarity : 0.003 0.033 1823 Dihedral : 5.508 66.814 1710 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 1.53 % Allowed : 16.97 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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 are not related in a simple way. whole: 0.60 (0.24), residues: 1291 helix: 1.92 (0.22), residues: 605 sheet: -1.11 (0.45), residues: 125 loop : -0.95 (0.27), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 503 TYR 0.010 0.001 TYR A 859 PHE 0.011 0.001 PHE A 783 TRP 0.004 0.001 TRP A 79 HIS 0.002 0.000 HIS A 483 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (10545) covalent geometry : angle 0.49916 / 0.25 (14311) SS BOND : bond 0.00101 / 0.03 ( 3) SS BOND : angle 0.48022 / 0.31 ( 6) hydrogen bonds : bond 0.03222 / 2.14 ( 536) hydrogen bonds : angle 4.36623 / 3.21 ( 1530) link_BETA1-4 : bond 0.00280 / 0.14 ( 2) link_BETA1-4 : angle 1.18553 / 0.65 ( 6) link_NAG-ASN : bond 0.00071 / 0.03 ( 3) link_NAG-ASN : angle 1.23046 / 0.57 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.556 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 GLU cc_start: 0.7700 (tt0) cc_final: 0.7122 (tt0) REVERT: A 368 THR cc_start: 0.8806 (m) cc_final: 0.8440 (p) outliers start: 17 outliers final: 14 residues processed: 109 average time/residue: 0.2359 time to fit residues: 37.1570 Evaluate side-chains 108 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 TRP Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 959 SER Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 158 ASN Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain C residue 55 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 58 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 chunk 95 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.123706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.079886 restraints weight = 63778.508| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 3.35 r_work: 0.3006 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10553 Z= 0.176 Angle : 0.520 6.055 14332 Z= 0.267 Chirality : 0.040 0.157 1640 Planarity : 0.003 0.034 1823 Dihedral : 5.528 66.990 1710 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.71 % Allowed : 17.41 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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 are not related in a simple way. whole: 0.56 (0.24), residues: 1291 helix: 1.88 (0.22), residues: 605 sheet: -1.14 (0.45), residues: 125 loop : -0.97 (0.27), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 420 TYR 0.012 0.001 TYR A 859 PHE 0.013 0.001 PHE A 783 TRP 0.004 0.001 TRP A 79 HIS 0.002 0.000 HIS A 483 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.18 (10545) covalent geometry : angle 0.51827 / 0.27 (14311) SS BOND : bond 0.00183 / 0.06 ( 3) SS BOND : angle 0.47923 / 0.30 ( 6) hydrogen bonds : bond 0.03275 / 2.16 ( 536) hydrogen bonds : angle 4.41679 / 3.25 ( 1530) link_BETA1-4 : bond 0.00263 / 0.13 ( 2) link_BETA1-4 : angle 1.15780 / 0.63 ( 6) link_NAG-ASN : bond 0.00158 / 0.06 ( 3) link_NAG-ASN : angle 1.35626 / 0.62 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.552 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLU cc_start: 0.9461 (tm-30) cc_final: 0.9242 (tm-30) REVERT: A 205 ASN cc_start: 0.8648 (m-40) cc_final: 0.8364 (m-40) REVERT: A 211 GLU cc_start: 0.7810 (tt0) cc_final: 0.7078 (tt0) outliers start: 19 outliers final: 18 residues processed: 110 average time/residue: 0.2293 time to fit residues: 36.3479 Evaluate side-chains 111 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 TRP Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 858 SER Chi-restraints excluded: chain A residue 959 SER Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 158 ASN Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain C residue 55 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 63 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 108 optimal weight: 0.5980 chunk 112 optimal weight: 0.3980 chunk 31 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 54 optimal weight: 20.0000 chunk 98 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 374 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 = 0.3938 r_free = 0.3938 target = 0.123882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.079489 restraints weight = 63953.365| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 3.40 r_work: 0.3004 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10553 Z= 0.170 Angle : 0.526 6.055 14332 Z= 0.271 Chirality : 0.040 0.156 1640 Planarity : 0.003 0.033 1823 Dihedral : 5.601 66.817 1710 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 1.53 % Allowed : 17.86 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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 are not related in a simple way. whole: 0.51 (0.24), residues: 1291 helix: 1.85 (0.22), residues: 605 sheet: -1.13 (0.45), residues: 125 loop : -1.01 (0.27), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 375 TYR 0.011 0.001 TYR A 859 PHE 0.012 0.001 PHE A 783 TRP 0.004 0.001 TRP A 79 HIS 0.002 0.000 HIS A 483 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 (10545) covalent geometry : angle 0.52511 / 0.27 (14311) SS BOND : bond 0.00184 / 0.06 ( 3) SS BOND : angle 0.50892 / 0.32 ( 6) hydrogen bonds : bond 0.03266 / 2.15 ( 536) hydrogen bonds : angle 4.39983 / 3.24 ( 1530) link_BETA1-4 : bond 0.00253 / 0.13 ( 2) link_BETA1-4 : angle 1.19594 / 0.66 ( 6) link_NAG-ASN : bond 0.00142 / 0.05 ( 3) link_NAG-ASN : angle 1.30965 / 0.60 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.537 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLU cc_start: 0.9467 (tm-30) cc_final: 0.9251 (tm-30) REVERT: A 205 ASN cc_start: 0.8721 (m-40) cc_final: 0.8491 (m-40) REVERT: A 211 GLU cc_start: 0.7873 (tt0) cc_final: 0.7119 (tt0) REVERT: A 381 MET cc_start: 0.5631 (mmm) cc_final: 0.5292 (mmm) REVERT: A 579 MET cc_start: 0.7873 (mmp) cc_final: 0.6833 (mmp) outliers start: 17 outliers final: 17 residues processed: 108 average time/residue: 0.2262 time to fit residues: 35.2106 Evaluate side-chains 109 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 TRP Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 858 SER Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 158 ASN Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain C residue 55 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 30.0000 chunk 20 optimal weight: 9.9990 chunk 30 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 47 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 374 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.123472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.079256 restraints weight = 63884.815| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 3.38 r_work: 0.2987 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10553 Z= 0.202 Angle : 0.539 6.149 14332 Z= 0.278 Chirality : 0.040 0.155 1640 Planarity : 0.003 0.033 1823 Dihedral : 5.582 67.700 1710 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 1.62 % Allowed : 17.95 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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 are not related in a simple way. whole: 0.47 (0.24), residues: 1291 helix: 1.83 (0.21), residues: 605 sheet: -1.16 (0.45), residues: 125 loop : -1.03 (0.27), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 375 TYR 0.012 0.001 TYR A 859 PHE 0.013 0.001 PHE A 783 TRP 0.004 0.001 TRP A 79 HIS 0.002 0.000 HIS A 483 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.20 (10545) covalent geometry : angle 0.53743 / 0.28 (14311) SS BOND : bond 0.00224 / 0.08 ( 3) SS BOND : angle 0.51525 / 0.32 ( 6) hydrogen bonds : bond 0.03328 / 2.19 ( 536) hydrogen bonds : angle 4.46528 / 3.29 ( 1530) link_BETA1-4 : bond 0.00225 / 0.11 ( 2) link_BETA1-4 : angle 1.18603 / 0.65 ( 6) link_NAG-ASN : bond 0.00195 / 0.07 ( 3) link_NAG-ASN : angle 1.35255 / 0.62 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.555 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLU cc_start: 0.9463 (tm-30) cc_final: 0.9251 (tm-30) REVERT: A 205 ASN cc_start: 0.8731 (m-40) cc_final: 0.8510 (m-40) REVERT: A 211 GLU cc_start: 0.7938 (tt0) cc_final: 0.7177 (tt0) REVERT: A 376 MET cc_start: 0.7980 (mmt) cc_final: 0.7627 (tpp) outliers start: 18 outliers final: 18 residues processed: 108 average time/residue: 0.2321 time to fit residues: 36.1673 Evaluate side-chains 110 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 TRP Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain A residue 598 SER Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 858 SER Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 158 ASN Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain C residue 55 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 92 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 0 optimal weight: 30.0000 chunk 9 optimal weight: 2.9990 chunk 96 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.124588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.080814 restraints weight = 63291.227| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 3.36 r_work: 0.3019 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10553 Z= 0.107 Angle : 0.509 5.984 14332 Z= 0.259 Chirality : 0.040 0.156 1640 Planarity : 0.003 0.033 1823 Dihedral : 5.472 68.201 1710 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 1.35 % Allowed : 18.13 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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 are not related in a simple way. whole: 0.65 (0.24), residues: 1291 helix: 1.93 (0.22), residues: 605 sheet: -0.98 (0.44), residues: 128 loop : -0.92 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 375 TYR 0.009 0.001 TYR A 859 PHE 0.010 0.001 PHE A 783 TRP 0.004 0.001 TRP A 79 HIS 0.002 0.000 HIS A 483 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (10545) covalent geometry : angle 0.50770 / 0.26 (14311) SS BOND : bond 0.00102 / 0.03 ( 3) SS BOND : angle 0.51399 / 0.34 ( 6) hydrogen bonds : bond 0.03164 / 2.09 ( 536) hydrogen bonds : angle 4.30928 / 3.17 ( 1530) link_BETA1-4 : bond 0.00259 / 0.13 ( 2) link_BETA1-4 : angle 1.23575 / 0.68 ( 6) link_NAG-ASN : bond 0.00094 / 0.04 ( 3) link_NAG-ASN : angle 1.15328 / 0.54 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2582 Ramachandran restraints generated. 1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.633 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 GLU cc_start: 0.9471 (tm-30) cc_final: 0.9266 (tm-30) REVERT: A 211 GLU cc_start: 0.7970 (tt0) cc_final: 0.7217 (tt0) REVERT: A 579 MET cc_start: 0.7931 (mmp) cc_final: 0.7118 (mmt) outliers start: 15 outliers final: 13 residues processed: 107 average time/residue: 0.2329 time to fit residues: 36.2287 Evaluate side-chains 105 residues out of total 1114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 158 ASN Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 194 GLU Chi-restraints excluded: chain B residue 205 ASN Chi-restraints excluded: chain B residue 295 PHE Chi-restraints excluded: chain C residue 55 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 47 optimal weight: 1.9990 chunk 2 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 12 optimal weight: 9.9990 chunk 102 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.124793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.080757 restraints weight = 63449.348| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 3.38 r_work: 0.3032 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10553 Z= 0.106 Angle : 0.506 8.148 14332 Z= 0.256 Chirality : 0.040 0.156 1640 Planarity : 0.003 0.033 1823 Dihedral : 5.362 67.875 1710 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 1.17 % Allowed : 18.31 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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 are not related in a simple way. whole: 0.71 (0.24), residues: 1291 helix: 1.99 (0.22), residues: 605 sheet: -0.96 (0.44), residues: 128 loop : -0.90 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 375 TYR 0.012 0.001 TYR B 199 PHE 0.009 0.001 PHE A 87 TRP 0.012 0.001 TRP A 79 HIS 0.002 0.000 HIS A 483 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (10545) covalent geometry : angle 0.50512 / 0.26 (14311) SS BOND : bond 0.00095 / 0.03 ( 3) SS BOND : angle 0.45108 / 0.29 ( 6) hydrogen bonds : bond 0.03072 / 2.04 ( 536) hydrogen bonds : angle 4.24870 / 3.13 ( 1530) link_BETA1-4 : bond 0.00314 / 0.16 ( 2) link_BETA1-4 : angle 1.17185 / 0.65 ( 6) link_NAG-ASN : bond 0.00086 / 0.04 ( 3) link_NAG-ASN : angle 1.16077 / 0.54 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4964.56 seconds wall clock time: 85 minutes 16.06 seconds (5116.06 seconds total)