Starting phenix.real_space_refine on Sat Aug 8 02:00:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v7l_43003/08_2026/8v7l_43003.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v7l_43003/08_2026/8v7l_43003.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8v7l_43003/08_2026/8v7l_43003.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v7l_43003/08_2026/8v7l_43003.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8v7l_43003/08_2026/8v7l_43003.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v7l_43003/08_2026/8v7l_43003.map" } resolution = 2.9 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= 0.005 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 27 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 282 5.49 5 Mg 1 5.21 5 S 34 5.16 5 C 8872 2.51 5 N 2861 2.21 5 O 3399 1.98 5 H 10096 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25545 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 1563 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 3, 'TRANS': 89} Chain: "B" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1468 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "C" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1730 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 1542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1542 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "E" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 1604 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "F" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 1349 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 1629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 1629 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "H" Number of atoms: 1486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 1486 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 2885 Classifications: {'DNA': 140} Link IDs: {'rna3p': 139} Chain: "J" Number of atoms: 2855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 2855 Classifications: {'DNA': 140} Link IDs: {'rna3p': 139} Chain: "W" Number of atoms: 7406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 7406 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 18, 'TRANS': 427} Chain breaks: 1 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.20, per 1000 atoms: 0.20 Number of scatterers: 25545 At special positions: 0 Unit cell: (147.343, 130.407, 116.012, 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 34 16.00 P 282 15.00 Mg 1 11.99 O 3399 8.00 N 2861 7.00 C 8872 6.00 H 10096 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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 Time building additional restraints: 2.44 Conformation dependent library (CDL) restraints added in 696.5 milliseconds 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2266 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 12 sheets defined 65.7% alpha, 5.7% beta 44 base pairs and 185 stacking pairs defined. Time for finding SS restraints: 4.49 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.581A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.502A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU A 70 " --> pdb=" O PRO A 66 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 113 removed outlier: 3.646A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.653A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 removed outlier: 3.666A pdb=" N LEU B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.503A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.600A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.868A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.691A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN C 84 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.732A pdb=" N GLN D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.634A pdb=" N ALA D 78 " --> pdb=" O ALA D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 120 removed outlier: 3.518A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 removed outlier: 3.534A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG E 49 " --> pdb=" O THR E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.636A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.570A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.689A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.532A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.513A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.611A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.569A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'H' and resid 34 through 46 removed outlier: 3.789A pdb=" N GLN H 44 " --> pdb=" O LYS H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 120 Processing helix chain 'W' and resid 181 through 198 removed outlier: 3.627A pdb=" N TYR W 195 " --> pdb=" O LEU W 191 " (cutoff:3.500A) Processing helix chain 'W' and resid 210 through 225 removed outlier: 3.801A pdb=" N GLN W 214 " --> pdb=" O GLY W 210 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS W 223 " --> pdb=" O LEU W 219 " (cutoff:3.500A) Processing helix chain 'W' and resid 237 through 239 No H-bonds generated for 'chain 'W' and resid 237 through 239' Processing helix chain 'W' and resid 240 through 252 Processing helix chain 'W' and resid 263 through 274 Processing helix chain 'W' and resid 286 through 293 removed outlier: 3.521A pdb=" N LEU W 290 " --> pdb=" O SER W 286 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE W 291 " --> pdb=" O TYR W 287 " (cutoff:3.500A) Processing helix chain 'W' and resid 293 through 300 removed outlier: 3.818A pdb=" N PHE W 297 " --> pdb=" O GLU W 293 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHE W 300 " --> pdb=" O VAL W 296 " (cutoff:3.500A) Processing helix chain 'W' and resid 310 through 314 removed outlier: 3.680A pdb=" N ILE W 313 " --> pdb=" O ALA W 310 " (cutoff:3.500A) Processing helix chain 'W' and resid 318 through 327 removed outlier: 3.805A pdb=" N PHE W 327 " --> pdb=" O ILE W 323 " (cutoff:3.500A) Processing helix chain 'W' and resid 343 through 355 removed outlier: 3.852A pdb=" N LEU W 347 " --> pdb=" O ASN W 343 " (cutoff:3.500A) Processing helix chain 'W' and resid 361 through 369 removed outlier: 4.396A pdb=" N SER W 367 " --> pdb=" O ASP W 363 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N TRP W 368 " --> pdb=" O ASP W 364 " (cutoff:3.500A) Processing helix chain 'W' and resid 387 through 391 removed outlier: 4.584A pdb=" N PHE W 391 " --> pdb=" O VAL W 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 387 through 391' Processing helix chain 'W' and resid 396 through 401 Processing helix chain 'W' and resid 417 through 430 Processing helix chain 'W' and resid 438 through 442 Processing helix chain 'W' and resid 448 through 459 removed outlier: 3.989A pdb=" N GLN W 452 " --> pdb=" O ASN W 448 " (cutoff:3.500A) Processing helix chain 'W' and resid 476 through 482 removed outlier: 3.761A pdb=" N THR W 480 " --> pdb=" O MET W 476 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER W 482 " --> pdb=" O LEU W 478 " (cutoff:3.500A) Processing helix chain 'W' and resid 482 through 487 Processing helix chain 'W' and resid 490 through 497 Processing helix chain 'W' and resid 508 through 523 removed outlier: 3.506A pdb=" N LEU W 512 " --> pdb=" O MET W 508 " (cutoff:3.500A) Processing helix chain 'W' and resid 534 through 547 removed outlier: 3.919A pdb=" N GLN W 539 " --> pdb=" O HIS W 535 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASP W 540 " --> pdb=" O ASP W 536 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N TYR W 545 " --> pdb=" O SER W 541 " (cutoff:3.500A) Processing helix chain 'W' and resid 558 through 563 Processing helix chain 'W' and resid 582 through 592 removed outlier: 3.989A pdb=" N ASP W 586 " --> pdb=" O ASN W 582 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA W 589 " --> pdb=" O VAL W 585 " (cutoff:3.500A) Processing helix chain 'W' and resid 612 through 629 removed outlier: 3.859A pdb=" N ARG W 616 " --> pdb=" O THR W 612 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU W 627 " --> pdb=" O MET W 623 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASP W 628 " --> pdb=" O LYS W 624 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.781A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.837A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.892A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.822A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 6.956A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'W' and resid 258 through 260 removed outlier: 6.248A pdb=" N HIS W 232 " --> pdb=" O CYS W 283 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N THR W 285 " --> pdb=" O HIS W 232 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N VAL W 234 " --> pdb=" O THR W 285 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N MET W 233 " --> pdb=" O VAL W 306 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ASP W 308 " --> pdb=" O MET W 233 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N LEU W 235 " --> pdb=" O ASP W 308 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ARG W 303 " --> pdb=" O ASN W 331 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N LEU W 333 " --> pdb=" O ARG W 303 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LEU W 305 " --> pdb=" O LEU W 333 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N LEU W 335 " --> pdb=" O LEU W 305 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE W 307 " --> pdb=" O LEU W 335 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N ILE W 202 " --> pdb=" O LEU W 393 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'W' and resid 408 through 414 removed outlier: 3.506A pdb=" N ARG W 606 " --> pdb=" O VAL W 410 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N VAL W 574 " --> pdb=" O PHE W 605 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N PHE W 607 " --> pdb=" O VAL W 574 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU W 576 " --> pdb=" O PHE W 607 " (cutoff:3.500A) removed outlier: 8.931A pdb=" N THR W 609 " --> pdb=" O LEU W 576 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N LEU W 503 " --> pdb=" O ILE W 575 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU W 557 " --> pdb=" O ILE W 504 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N CYS W 527 " --> pdb=" O MET W 556 " (cutoff:3.500A) 521 hydrogen bonds defined for protein. 1530 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 100 hydrogen bonds 200 hydrogen bond angles 0 basepair planarities 44 basepair parallelities 185 stacking parallelities Total time for adding SS restraints: 6.76 Time building geometry restraints manager: 3.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.01: 10090 1.01 - 1.21: 224 1.21 - 1.41: 6465 1.41 - 1.61: 9550 1.61 - 1.82: 72 Bond restraints: 26401 Sorted by residual: bond pdb=" SG CYS W 527 " pdb=" HG CYS W 527 " ideal model delta sigma weight residual 1.200 1.341 -0.141 2.00e-02 2.50e+03 4.98e+01 bond pdb=" SG CYS W 259 " pdb=" HG CYS W 259 " ideal model delta sigma weight residual 1.200 1.340 -0.140 2.00e-02 2.50e+03 4.90e+01 bond pdb=" SG CYS W 283 " pdb=" HG CYS W 283 " ideal model delta sigma weight residual 1.200 1.340 -0.140 2.00e-02 2.50e+03 4.87e+01 bond pdb=" SG CYS W 457 " pdb=" HG CYS W 457 " ideal model delta sigma weight residual 1.200 1.339 -0.139 2.00e-02 2.50e+03 4.85e+01 bond pdb=" SG CYS W 456 " pdb=" HG CYS W 456 " ideal model delta sigma weight residual 1.200 1.339 -0.139 2.00e-02 2.50e+03 4.82e+01 ... (remaining 26396 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 42092 2.50 - 5.01: 3409 5.01 - 7.51: 501 7.51 - 10.01: 57 10.01 - 12.52: 7 Bond angle restraints: 46066 Sorted by residual: angle pdb=" N HIS B 18 " pdb=" CA HIS B 18 " pdb=" C HIS B 18 " ideal model delta sigma weight residual 111.30 123.82 -12.52 1.43e+00 4.89e-01 7.66e+01 angle pdb=" N GLY D 101 " pdb=" CA GLY D 101 " pdb=" C GLY D 101 " ideal model delta sigma weight residual 112.73 122.49 -9.76 1.20e+00 6.94e-01 6.62e+01 angle pdb=" N ARG E 83 " pdb=" CA ARG E 83 " pdb=" C ARG E 83 " ideal model delta sigma weight residual 109.95 98.72 11.23 1.44e+00 4.82e-01 6.09e+01 angle pdb=" N GLY W 565 " pdb=" CA GLY W 565 " pdb=" C GLY W 565 " ideal model delta sigma weight residual 115.42 125.03 -9.61 1.27e+00 6.20e-01 5.73e+01 angle pdb=" N ASP W 610 " pdb=" CA ASP W 610 " pdb=" C ASP W 610 " ideal model delta sigma weight residual 111.28 119.04 -7.76 1.09e+00 8.42e-01 5.07e+01 ... (remaining 46061 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.65: 10959 29.65 - 59.30: 1195 59.30 - 88.95: 66 88.95 - 118.59: 4 118.59 - 148.24: 2 Dihedral angle restraints: 12226 sinusoidal: 8223 harmonic: 4003 Sorted by residual: dihedral pdb=" O1B ADP W1101 " pdb=" O3A ADP W1101 " pdb=" PB ADP W1101 " pdb=" PA ADP W1101 " ideal model delta sinusoidal sigma weight residual 300.00 170.38 129.61 1 2.00e+01 2.50e-03 3.93e+01 dihedral pdb=" C5' ADP W1101 " pdb=" O5' ADP W1101 " pdb=" PA ADP W1101 " pdb=" O2A ADP W1101 " ideal model delta sinusoidal sigma weight residual -60.00 -156.68 96.69 1 2.00e+01 2.50e-03 2.68e+01 dihedral pdb=" CA PRO H 100 " pdb=" C PRO H 100 " pdb=" N GLY H 101 " pdb=" CA GLY H 101 " ideal model delta harmonic sigma weight residual -180.00 -158.73 -21.27 0 5.00e+00 4.00e-02 1.81e+01 ... (remaining 12223 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 1981 0.104 - 0.207: 571 0.207 - 0.311: 70 0.311 - 0.414: 5 0.414 - 0.518: 2 Chirality restraints: 2629 Sorted by residual: chirality pdb=" CA ARG E 40 " pdb=" N ARG E 40 " pdb=" C ARG E 40 " pdb=" CB ARG E 40 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.70e+00 chirality pdb=" C3' DC I 80 " pdb=" C4' DC I 80 " pdb=" O3' DC I 80 " pdb=" C2' DC I 80 " both_signs ideal model delta sigma weight residual False -2.73 -2.31 -0.42 2.00e-01 2.50e+01 4.34e+00 chirality pdb=" CA LYS D 82 " pdb=" N LYS D 82 " pdb=" C LYS D 82 " pdb=" CB LYS D 82 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.17e+00 ... (remaining 2626 not shown) Planarity restraints: 3112 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN W 481 " 0.211 2.00e-02 2.50e+03 4.71e-01 3.33e+03 pdb=" CG ASN W 481 " -0.013 2.00e-02 2.50e+03 pdb=" OD1 ASN W 481 " -0.208 2.00e-02 2.50e+03 pdb=" ND2 ASN W 481 " 0.003 2.00e-02 2.50e+03 pdb="HD21 ASN W 481 " -0.786 2.00e-02 2.50e+03 pdb="HD22 ASN W 481 " 0.792 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN W 352 " 0.226 2.00e-02 2.50e+03 4.69e-01 3.30e+03 pdb=" CG ASN W 352 " -0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN W 352 " -0.220 2.00e-02 2.50e+03 pdb=" ND2 ASN W 352 " -0.002 2.00e-02 2.50e+03 pdb="HD21 ASN W 352 " 0.788 2.00e-02 2.50e+03 pdb="HD22 ASN W 352 " -0.774 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 38 " -0.055 2.00e-02 2.50e+03 4.29e-01 2.76e+03 pdb=" CG ASN C 38 " -0.000 2.00e-02 2.50e+03 pdb=" OD1 ASN C 38 " 0.054 2.00e-02 2.50e+03 pdb=" ND2 ASN C 38 " -0.000 2.00e-02 2.50e+03 pdb="HD21 ASN C 38 " -0.740 2.00e-02 2.50e+03 pdb="HD22 ASN C 38 " 0.741 2.00e-02 2.50e+03 ... (remaining 3109 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.10: 197 2.10 - 2.72: 33674 2.72 - 3.35: 62847 3.35 - 3.97: 85843 3.97 - 4.60: 132869 Nonbonded interactions: 315430 Sorted by model distance: nonbonded pdb=" HE2 LYS E 64 " pdb=" HE1 MET E 90 " model vdw 1.469 2.440 nonbonded pdb="HH11 ARG G 11 " pdb=" O4' DG I 92 " model vdw 1.768 2.450 nonbonded pdb=" H VAL E 117 " pdb=" OP1 DA I 131 " model vdw 1.788 2.450 nonbonded pdb=" HH TYR G 57 " pdb=" OE2 GLU G 61 " model vdw 1.799 2.450 nonbonded pdb=" HH TYR H 37 " pdb=" OP1 DG J 122 " model vdw 1.804 2.450 ... (remaining 315425 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' selection = (chain 'E' and resid 41 through 133) } ncs_group { reference = (chain 'B' and resid 21 through 102) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 11 through 112) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 28 through 120) selection = chain 'H' } 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 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: 4.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.180 Extract box with map and model: 0.510 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 30.700 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:8.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5718 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 : 0.011 0.067 16305 Z= 0.807 Angle : 1.411 12.516 23222 Z= 1.007 Chirality : 0.088 0.518 2629 Planarity : 0.010 0.111 1958 Dihedral : 21.509 148.243 6838 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.55 % Favored : 96.20 % Rotamer: Outliers : 2.32 % Allowed : 3.57 % Favored : 94.11 % 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 are not related in a simple way. whole: -1.48 (0.21), residues: 1183 helix: -0.48 (0.17), residues: 727 sheet: -0.72 (0.59), residues: 68 loop : -1.79 (0.27), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 35 TYR 0.116 0.008 TYR G 57 PHE 0.041 0.006 PHE H 67 TRP 0.014 0.002 TRP W 190 HIS 0.011 0.003 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.01071 / 0.81 (16305) covalent geometry : angle 1.41076 / 1.01 (23222) hydrogen bonds : bond 0.25835 / 17.08 ( 621) hydrogen bonds : angle 8.26816 / 6.07 ( 1730) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 248 time to evaluate : 0.634 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: C 90 ASP cc_start: 0.7835 (t70) cc_final: 0.7439 (t0) REVERT: W 348 TRP cc_start: 0.7678 (t60) cc_final: 0.7305 (t60) REVERT: W 508 MET cc_start: 0.7289 (mtt) cc_final: 0.6772 (ttm) outliers start: 24 outliers final: 6 residues processed: 267 average time/residue: 1.6732 time to fit residues: 478.0400 Evaluate side-chains 127 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 121 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain W residue 283 CYS Chi-restraints excluded: chain W residue 456 CYS Chi-restraints excluded: chain W residue 459 HIS Chi-restraints excluded: chain W residue 558 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN F 25 ASN F 75 HIS H 92 GLN W 342 ASN W 345 HIS ** W 477 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 = 0.4147 r_free = 0.4147 target = 0.115544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.092759 restraints weight = 104707.122| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 2.03 r_work: 0.3534 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16305 Z= 0.200 Angle : 0.698 7.822 23222 Z= 0.425 Chirality : 0.042 0.212 2629 Planarity : 0.006 0.055 1958 Dihedral : 24.743 163.103 4409 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.54 % Favored : 97.38 % Rotamer: Outliers : 2.41 % Allowed : 15.44 % Favored : 82.14 % 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 are not related in a simple way. whole: -0.06 (0.23), residues: 1183 helix: 1.00 (0.19), residues: 728 sheet: -0.73 (0.59), residues: 78 loop : -1.95 (0.26), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 42 TYR 0.014 0.002 TYR W 524 PHE 0.013 0.002 PHE W 359 TRP 0.011 0.002 TRP W 348 HIS 0.012 0.002 HIS W 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.20 (16305) covalent geometry : angle 0.69821 / 0.43 (23222) hydrogen bonds : bond 0.08956 / 5.83 ( 621) hydrogen bonds : angle 4.78368 / 3.42 ( 1730) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 121 time to evaluate : 0.688 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: A 64 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.8160 (mttp) REVERT: C 90 ASP cc_start: 0.8087 (t0) cc_final: 0.7825 (t0) REVERT: D 54 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.7782 (tmtm) REVERT: E 120 MET cc_start: 0.7500 (OUTLIER) cc_final: 0.6466 (mpp) REVERT: G 99 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.7565 (mtt180) REVERT: W 207 MET cc_start: 0.7652 (mtm) cc_final: 0.7122 (mtm) REVERT: W 508 MET cc_start: 0.7237 (mtt) cc_final: 0.6173 (ttm) outliers start: 25 outliers final: 9 residues processed: 138 average time/residue: 1.4344 time to fit residues: 214.9754 Evaluate side-chains 128 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain W residue 174 TYR Chi-restraints excluded: chain W residue 191 LEU Chi-restraints excluded: chain W residue 224 HIS Chi-restraints excluded: chain W residue 282 VAL Chi-restraints excluded: chain W residue 283 CYS Chi-restraints excluded: chain W residue 311 HIS Chi-restraints excluded: chain W residue 456 CYS Chi-restraints excluded: chain W residue 500 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 107 optimal weight: 7.9990 chunk 110 optimal weight: 0.8980 chunk 95 optimal weight: 10.0000 chunk 139 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 122 optimal weight: 10.0000 chunk 7 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** W 481 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 = 0.4039 r_free = 0.4039 target = 0.109649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.085454 restraints weight = 101775.645| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 1.95 r_work: 0.3379 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.3943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 16305 Z= 0.183 Angle : 0.648 9.522 23222 Z= 0.382 Chirality : 0.040 0.232 2629 Planarity : 0.005 0.053 1958 Dihedral : 26.044 165.992 4405 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.38 % Favored : 96.53 % Rotamer: Outliers : 1.64 % Allowed : 16.51 % Favored : 81.85 % 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 are not related in a simple way. whole: 0.59 (0.24), residues: 1183 helix: 1.64 (0.19), residues: 724 sheet: -0.87 (0.59), residues: 78 loop : -1.83 (0.27), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 42 TYR 0.019 0.002 TYR G 50 PHE 0.023 0.001 PHE W 391 TRP 0.011 0.001 TRP W 348 HIS 0.004 0.001 HIS W 535 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.18 (16305) covalent geometry : angle 0.64836 / 0.38 (23222) hydrogen bonds : bond 0.07080 / 4.66 ( 621) hydrogen bonds : angle 4.28920 / 3.06 ( 1730) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 120 MET cc_start: 0.7601 (OUTLIER) cc_final: 0.7364 (mtt) REVERT: G 99 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.7508 (mtt180) REVERT: W 222 MET cc_start: 0.5390 (OUTLIER) cc_final: 0.5067 (mtt) REVERT: W 508 MET cc_start: 0.7226 (mtt) cc_final: 0.6195 (ttm) REVERT: W 527 CYS cc_start: 0.8171 (t) cc_final: 0.7708 (t) REVERT: W 555 PHE cc_start: 0.7605 (t80) cc_final: 0.6932 (t80) outliers start: 17 outliers final: 4 residues processed: 132 average time/residue: 1.4080 time to fit residues: 202.3744 Evaluate side-chains 124 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 117 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain W residue 222 MET Chi-restraints excluded: chain W residue 224 HIS Chi-restraints excluded: chain W residue 283 CYS Chi-restraints excluded: chain W residue 456 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 81 optimal weight: 9.9990 chunk 132 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 131 optimal weight: 7.9990 chunk 19 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 72 optimal weight: 40.0000 chunk 18 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN C 104 GLN F 93 GLN W 227 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.105653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.081121 restraints weight = 99947.809| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.96 r_work: 0.3286 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.4419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16305 Z= 0.206 Angle : 0.605 8.439 23222 Z= 0.362 Chirality : 0.038 0.232 2629 Planarity : 0.004 0.056 1958 Dihedral : 26.286 160.866 4404 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.54 % Favored : 97.38 % Rotamer: Outliers : 2.03 % Allowed : 16.51 % Favored : 81.47 % 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 are not related in a simple way. whole: 0.64 (0.24), residues: 1183 helix: 1.73 (0.19), residues: 726 sheet: -0.92 (0.58), residues: 78 loop : -1.94 (0.27), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG W 528 TYR 0.010 0.001 TYR W 424 PHE 0.013 0.001 PHE W 353 TRP 0.009 0.001 TRP W 348 HIS 0.004 0.001 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.21 (16305) covalent geometry : angle 0.60530 / 0.36 (23222) hydrogen bonds : bond 0.06733 / 4.41 ( 621) hydrogen bonds : angle 4.18321 / 2.97 ( 1730) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 75 LYS cc_start: 0.9146 (mtmt) cc_final: 0.8901 (mtpm) REVERT: G 99 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.7493 (mtt180) REVERT: W 222 MET cc_start: 0.5452 (OUTLIER) cc_final: 0.5186 (mtt) REVERT: W 508 MET cc_start: 0.7294 (mtt) cc_final: 0.6230 (ttm) REVERT: W 527 CYS cc_start: 0.8059 (t) cc_final: 0.7496 (t) REVERT: W 555 PHE cc_start: 0.7810 (t80) cc_final: 0.7100 (t80) REVERT: W 556 MET cc_start: 0.5549 (mtm) cc_final: 0.5027 (ptp) outliers start: 21 outliers final: 8 residues processed: 130 average time/residue: 1.3828 time to fit residues: 195.8525 Evaluate side-chains 128 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain W residue 191 LEU Chi-restraints excluded: chain W residue 222 MET Chi-restraints excluded: chain W residue 271 VAL Chi-restraints excluded: chain W residue 283 CYS Chi-restraints excluded: chain W residue 456 CYS Chi-restraints excluded: chain W residue 550 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 35 optimal weight: 0.9980 chunk 135 optimal weight: 8.9990 chunk 118 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 15 optimal weight: 0.2980 chunk 82 optimal weight: 10.0000 chunk 95 optimal weight: 9.9990 chunk 132 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 86 optimal weight: 20.0000 chunk 115 optimal weight: 5.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.103055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.077950 restraints weight = 99456.407| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.09 r_work: 0.3210 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.4967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16305 Z= 0.215 Angle : 0.634 7.774 23222 Z= 0.368 Chirality : 0.040 0.213 2629 Planarity : 0.005 0.059 1958 Dihedral : 26.900 163.085 4404 Min Nonbonded Distance : 1.725 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.55 % Favored : 96.37 % Rotamer: Outliers : 1.74 % Allowed : 16.89 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.63 (0.24), residues: 1183 helix: 1.71 (0.19), residues: 729 sheet: -0.97 (0.58), residues: 78 loop : -1.94 (0.27), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 63 TYR 0.011 0.001 TYR W 424 PHE 0.021 0.001 PHE W 391 TRP 0.008 0.001 TRP W 244 HIS 0.006 0.001 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.21 (16305) covalent geometry : angle 0.63375 / 0.37 (23222) hydrogen bonds : bond 0.06784 / 4.47 ( 621) hydrogen bonds : angle 4.11350 / 2.94 ( 1730) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 61 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7828 (tp30) REVERT: C 75 LYS cc_start: 0.9216 (mtmt) cc_final: 0.8909 (mtpm) REVERT: F 84 MET cc_start: 0.8505 (mmm) cc_final: 0.8273 (mmp) REVERT: G 99 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.7454 (mtt180) REVERT: W 222 MET cc_start: 0.5293 (OUTLIER) cc_final: 0.5061 (mtt) REVERT: W 508 MET cc_start: 0.7244 (mtt) cc_final: 0.6132 (ttm) REVERT: W 556 MET cc_start: 0.5671 (mtm) cc_final: 0.5058 (ptp) REVERT: W 591 ASP cc_start: 0.7659 (OUTLIER) cc_final: 0.7404 (t0) outliers start: 18 outliers final: 6 residues processed: 138 average time/residue: 1.3779 time to fit residues: 207.4936 Evaluate side-chains 128 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 119 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain W residue 191 LEU Chi-restraints excluded: chain W residue 222 MET Chi-restraints excluded: chain W residue 283 CYS Chi-restraints excluded: chain W residue 456 CYS Chi-restraints excluded: chain W residue 550 SER Chi-restraints excluded: chain W residue 591 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 59 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 51 optimal weight: 0.5980 chunk 106 optimal weight: 2.9990 chunk 133 optimal weight: 10.0000 chunk 53 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 73 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 = 0.3944 r_free = 0.3944 target = 0.103974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.079261 restraints weight = 99797.062| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.99 r_work: 0.3251 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.5085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 16305 Z= 0.135 Angle : 0.547 6.690 23222 Z= 0.330 Chirality : 0.035 0.207 2629 Planarity : 0.004 0.058 1958 Dihedral : 26.792 163.051 4404 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.54 % Favored : 97.38 % Rotamer: Outliers : 0.87 % Allowed : 17.86 % Favored : 81.27 % 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 are not related in a simple way. whole: 0.93 (0.25), residues: 1183 helix: 2.00 (0.19), residues: 728 sheet: -0.98 (0.59), residues: 78 loop : -1.89 (0.28), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 17 TYR 0.011 0.001 TYR F 51 PHE 0.008 0.001 PHE W 353 TRP 0.008 0.001 TRP W 521 HIS 0.004 0.001 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.14 (16305) covalent geometry : angle 0.54659 / 0.33 (23222) hydrogen bonds : bond 0.05624 / 3.72 ( 621) hydrogen bonds : angle 3.91638 / 2.78 ( 1730) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 125 time to evaluate : 0.830 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: C 75 LYS cc_start: 0.9195 (mtmt) cc_final: 0.8880 (mtpm) REVERT: F 84 MET cc_start: 0.8450 (mmm) cc_final: 0.8200 (mmp) REVERT: G 99 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.7428 (mtt180) REVERT: W 222 MET cc_start: 0.5313 (OUTLIER) cc_final: 0.5103 (mtt) REVERT: W 556 MET cc_start: 0.5647 (mtm) cc_final: 0.5121 (ptp) outliers start: 9 outliers final: 4 residues processed: 133 average time/residue: 1.3876 time to fit residues: 201.4809 Evaluate side-chains 127 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 121 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain W residue 191 LEU Chi-restraints excluded: chain W residue 222 MET Chi-restraints excluded: chain W residue 304 TYR Chi-restraints excluded: chain W residue 456 CYS Chi-restraints excluded: chain W residue 550 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 42 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 128 optimal weight: 9.9990 chunk 127 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 73 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 = 0.3936 r_free = 0.3936 target = 0.103477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.078581 restraints weight = 99283.488| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.03 r_work: 0.3235 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.5265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16305 Z= 0.150 Angle : 0.555 9.087 23222 Z= 0.327 Chirality : 0.035 0.199 2629 Planarity : 0.004 0.059 1958 Dihedral : 26.870 161.208 4403 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.38 % Favored : 96.53 % Rotamer: Outliers : 1.06 % Allowed : 17.66 % Favored : 81.27 % 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 are not related in a simple way. whole: 1.06 (0.25), residues: 1183 helix: 2.12 (0.19), residues: 728 sheet: -0.98 (0.59), residues: 78 loop : -1.87 (0.28), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG W 522 TYR 0.009 0.001 TYR W 424 PHE 0.017 0.001 PHE W 391 TRP 0.015 0.001 TRP W 521 HIS 0.024 0.001 HIS W 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.15 (16305) covalent geometry : angle 0.55455 / 0.33 (23222) hydrogen bonds : bond 0.05548 / 3.67 ( 621) hydrogen bonds : angle 3.81654 / 2.72 ( 1730) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 0.668 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: C 75 LYS cc_start: 0.9217 (mtmt) cc_final: 0.8899 (mtpm) REVERT: G 99 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.7438 (mtt180) REVERT: W 508 MET cc_start: 0.7133 (mtt) cc_final: 0.6096 (ttm) REVERT: W 527 CYS cc_start: 0.8166 (t) cc_final: 0.7700 (t) REVERT: W 555 PHE cc_start: 0.7875 (t80) cc_final: 0.7524 (t80) REVERT: W 556 MET cc_start: 0.5649 (mtm) cc_final: 0.5116 (ptp) REVERT: W 591 ASP cc_start: 0.7604 (OUTLIER) cc_final: 0.7388 (t0) outliers start: 11 outliers final: 4 residues processed: 134 average time/residue: 1.3657 time to fit residues: 199.1450 Evaluate side-chains 127 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 121 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain W residue 191 LEU Chi-restraints excluded: chain W residue 304 TYR Chi-restraints excluded: chain W residue 550 SER Chi-restraints excluded: chain W residue 591 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 138 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 102 optimal weight: 8.9990 chunk 3 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 62 optimal weight: 0.0170 chunk 58 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 97 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 overall best weight: 1.3424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** W 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 477 HIS ** 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 = 0.3928 r_free = 0.3928 target = 0.103027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.077896 restraints weight = 99328.735| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.07 r_work: 0.3222 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.5468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16305 Z= 0.154 Angle : 0.546 7.279 23222 Z= 0.323 Chirality : 0.035 0.170 2629 Planarity : 0.004 0.059 1958 Dihedral : 27.040 160.970 4402 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.79 % Favored : 97.13 % Rotamer: Outliers : 1.06 % Allowed : 18.63 % Favored : 80.31 % 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 are not related in a simple way. whole: 1.16 (0.25), residues: 1183 helix: 2.20 (0.19), residues: 728 sheet: -0.94 (0.60), residues: 78 loop : -1.84 (0.29), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 17 TYR 0.013 0.001 TYR W 304 PHE 0.008 0.001 PHE F 100 TRP 0.008 0.001 TRP W 348 HIS 0.013 0.001 HIS W 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.15 (16305) covalent geometry : angle 0.54564 / 0.32 (23222) hydrogen bonds : bond 0.05534 / 3.65 ( 621) hydrogen bonds : angle 3.76010 / 2.68 ( 1730) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 36 LYS cc_start: 0.9069 (OUTLIER) cc_final: 0.8407 (mtpp) REVERT: C 61 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7925 (tp30) REVERT: C 75 LYS cc_start: 0.9207 (mtmt) cc_final: 0.8857 (mtpm) REVERT: G 99 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.7428 (mtt180) REVERT: W 508 MET cc_start: 0.7115 (mtt) cc_final: 0.6003 (ttp) REVERT: W 556 MET cc_start: 0.5658 (mtm) cc_final: 0.5070 (ptp) REVERT: W 591 ASP cc_start: 0.7642 (OUTLIER) cc_final: 0.7294 (t0) outliers start: 11 outliers final: 3 residues processed: 134 average time/residue: 1.3977 time to fit residues: 203.6153 Evaluate side-chains 128 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 122 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain W residue 191 LEU Chi-restraints excluded: chain W residue 550 SER Chi-restraints excluded: chain W residue 591 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 81 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 108 optimal weight: 9.9990 chunk 109 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 89 optimal weight: 10.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... W 420 GLN ** W 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.101980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.076720 restraints weight = 99008.616| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.01 r_work: 0.3195 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.5673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16305 Z= 0.194 Angle : 0.582 8.159 23222 Z= 0.337 Chirality : 0.037 0.160 2629 Planarity : 0.004 0.060 1958 Dihedral : 27.215 159.759 4402 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.06 % Favored : 95.86 % Rotamer: Outliers : 1.25 % Allowed : 18.24 % Favored : 80.50 % 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 are not related in a simple way. whole: 1.02 (0.25), residues: 1183 helix: 2.09 (0.19), residues: 728 sheet: -0.98 (0.60), residues: 78 loop : -1.90 (0.28), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 17 TYR 0.011 0.001 TYR W 526 PHE 0.016 0.001 PHE W 391 TRP 0.015 0.002 TRP W 521 HIS 0.010 0.001 HIS W 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.19 (16305) covalent geometry : angle 0.58203 / 0.34 (23222) hydrogen bonds : bond 0.06034 / 3.98 ( 621) hydrogen bonds : angle 3.82797 / 2.74 ( 1730) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 36 LYS cc_start: 0.9078 (OUTLIER) cc_final: 0.8404 (mtpp) REVERT: C 61 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7920 (tp30) REVERT: C 75 LYS cc_start: 0.9227 (mtmt) cc_final: 0.8882 (mtpm) REVERT: G 99 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.7457 (mtt180) REVERT: W 508 MET cc_start: 0.7116 (mtt) cc_final: 0.6029 (ttp) REVERT: W 556 MET cc_start: 0.5722 (mtm) cc_final: 0.5170 (ptp) REVERT: W 591 ASP cc_start: 0.7638 (OUTLIER) cc_final: 0.7315 (t0) outliers start: 13 outliers final: 5 residues processed: 132 average time/residue: 1.2947 time to fit residues: 186.4710 Evaluate side-chains 127 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 119 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain W residue 191 LEU Chi-restraints excluded: chain W residue 550 SER Chi-restraints excluded: chain W residue 591 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 109 optimal weight: 5.9990 chunk 79 optimal weight: 20.0000 chunk 5 optimal weight: 2.9990 chunk 87 optimal weight: 20.0000 chunk 112 optimal weight: 4.9990 chunk 129 optimal weight: 8.9990 chunk 16 optimal weight: 0.5980 chunk 89 optimal weight: 9.9990 chunk 125 optimal weight: 9.9990 chunk 126 optimal weight: 0.4980 chunk 22 optimal weight: 0.3980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.101676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.076434 restraints weight = 98565.732| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.03 r_work: 0.3192 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.5801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16305 Z= 0.181 Angle : 0.568 7.362 23222 Z= 0.332 Chirality : 0.036 0.166 2629 Planarity : 0.004 0.060 1958 Dihedral : 27.342 160.905 4402 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.72 % Favored : 96.20 % Rotamer: Outliers : 1.25 % Allowed : 18.24 % Favored : 80.50 % 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 are not related in a simple way. whole: 0.97 (0.25), residues: 1183 helix: 2.07 (0.19), residues: 728 sheet: -0.93 (0.61), residues: 78 loop : -1.99 (0.28), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 17 TYR 0.010 0.001 TYR W 526 PHE 0.011 0.001 PHE W 353 TRP 0.009 0.001 TRP W 521 HIS 0.014 0.001 HIS W 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.18 (16305) covalent geometry : angle 0.56795 / 0.33 (23222) hydrogen bonds : bond 0.05937 / 3.93 ( 621) hydrogen bonds : angle 3.84118 / 2.74 ( 1730) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 52 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7911 (mp0) REVERT: C 36 LYS cc_start: 0.9083 (OUTLIER) cc_final: 0.8454 (mtpp) REVERT: C 61 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7973 (tp30) REVERT: C 75 LYS cc_start: 0.9220 (mtmt) cc_final: 0.8873 (mtpm) REVERT: G 99 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.7458 (mtt180) REVERT: W 508 MET cc_start: 0.7150 (mtt) cc_final: 0.6038 (ttp) REVERT: W 556 MET cc_start: 0.5770 (mtm) cc_final: 0.5191 (ptp) REVERT: W 591 ASP cc_start: 0.7649 (OUTLIER) cc_final: 0.7303 (t0) outliers start: 13 outliers final: 7 residues processed: 134 average time/residue: 1.2531 time to fit residues: 183.0133 Evaluate side-chains 130 residues out of total 1036 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 119 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain G residue 99 ARG Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain W residue 191 LEU Chi-restraints excluded: chain W residue 304 TYR Chi-restraints excluded: chain W residue 324 VAL Chi-restraints excluded: chain W residue 550 SER Chi-restraints excluded: chain W residue 591 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 138 optimal weight: 0.0970 chunk 56 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 98 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 123 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 45 optimal weight: 0.0470 overall best weight: 0.5676 ------------------------------------------------------------------------------- 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 = 0.3929 r_free = 0.3929 target = 0.102943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.077867 restraints weight = 98504.678| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.05 r_work: 0.3227 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.5869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16305 Z= 0.126 Angle : 0.535 7.623 23222 Z= 0.315 Chirality : 0.034 0.155 2629 Planarity : 0.004 0.059 1958 Dihedral : 27.209 161.833 4402 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.63 % Favored : 96.28 % Rotamer: Outliers : 0.68 % Allowed : 19.11 % Favored : 80.21 % 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 are not related in a simple way. whole: 1.26 (0.25), residues: 1183 helix: 2.30 (0.19), residues: 729 sheet: -0.87 (0.60), residues: 78 loop : -1.87 (0.28), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 17 TYR 0.009 0.001 TYR F 51 PHE 0.015 0.001 PHE W 391 TRP 0.007 0.001 TRP W 521 HIS 0.007 0.001 HIS W 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.13 (16305) covalent geometry : angle 0.53452 / 0.32 (23222) hydrogen bonds : bond 0.05105 / 3.38 ( 621) hydrogen bonds : angle 3.69562 / 2.63 ( 1730) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7838.81 seconds wall clock time: 133 minutes 28.93 seconds (8008.93 seconds total)