Starting phenix.real_space_refine on Fri Oct 23 00:50:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9txk_56399/10_2026/9txk_56399.cif Found real_map, /net/cci-nas-00/data/ceres_data/9txk_56399/10_2026/9txk_56399.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9txk_56399/10_2026/9txk_56399.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9txk_56399/10_2026/9txk_56399.map" model { file = "/net/cci-nas-00/data/ceres_data/9txk_56399/10_2026/9txk_56399.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9txk_56399/10_2026/9txk_56399.cif" } resolution = 3.3 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= 0.025 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: 5 Type Number sf(0) Gaussians Mg 1 5.21 5 S 27 5.16 5 C 4466 2.51 5 N 1175 2.21 5 O 1387 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7056 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3803 Classifications: {'peptide': 483} Link IDs: {'PTRANS': 18, 'TRANS': 464} Chain breaks: 4 Chain: "D" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1552 Classifications: {'peptide': 205} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 190} Chain breaks: 2 Chain: "E" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1642 Classifications: {'peptide': 210} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 198} Chain: "B" 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: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 31 Unusual residues: {' MG': 1, 'NAG': 2} Classifications: {'undetermined': 3, 'water': 2} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.71, per 1000 atoms: 0.24 Number of scatterers: 7056 At special positions: 0 Unit cell: (71.52, 104.3, 132.61, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 27 16.00 Mg 1 11.99 O 1387 8.00 N 1175 7.00 C 4466 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS D 21 " - pdb=" SG CYS D 95 " distance=2.04 Simple disulfide: pdb=" SG CYS D 142 " - pdb=" SG CYS D 197 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 193 " distance=2.04 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 B 1 " - " NAG B 2 " NAG-ASN " NAG A 701 " - " ASN A 207 " " NAG A 702 " - " ASN A 81 " " NAG B 1 " - " ASN A 577 " Time building additional restraints: 0.48 Conformation dependent library (CDL) restraints added in 412.7 milliseconds 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1688 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 15 sheets defined 19.9% alpha, 42.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 98 through 111 removed outlier: 3.622A pdb=" N GLN A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 287 through 303 removed outlier: 3.684A pdb=" N GLN A 291 " --> pdb=" O GLY A 287 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP A 302 " --> pdb=" O ILE A 298 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASP A 303 " --> pdb=" O LYS A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 342 Processing helix chain 'A' and resid 351 through 369 removed outlier: 4.070A pdb=" N ALA A 355 " --> pdb=" O ASN A 351 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA A 359 " --> pdb=" O ALA A 355 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL A 360 " --> pdb=" O MET A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 407 removed outlier: 3.745A pdb=" N ILE A 398 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 432 removed outlier: 3.736A pdb=" N LYS A 428 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP A 432 " --> pdb=" O LYS A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 450 Processing helix chain 'A' and resid 452 through 457 removed outlier: 3.560A pdb=" N GLU A 456 " --> pdb=" O ASP A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 540 Processing helix chain 'A' and resid 542 through 560 removed outlier: 3.617A pdb=" N ALA A 549 " --> pdb=" O GLU A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 563 No H-bonds generated for 'chain 'A' and resid 561 through 563' Processing helix chain 'A' and resid 564 through 583 Processing helix chain 'D' and resid 86 through 90 removed outlier: 4.092A pdb=" N SER D 90 " --> pdb=" O SER D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 190 No H-bonds generated for 'chain 'D' and resid 188 through 190' Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.739A pdb=" N ILE E 83 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 127 Processing helix chain 'E' and resid 181 through 187 Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 92 removed outlier: 5.798A pdb=" N ALA A 77 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N LEU A 149 " --> pdb=" O ALA A 77 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N ILE A 79 " --> pdb=" O GLU A 147 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLU A 147 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N PHE A 48 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N VAL A 44 " --> pdb=" O PHE A 48 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N HIS A 50 " --> pdb=" O SER A 42 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N SER A 42 " --> pdb=" O HIS A 50 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL A 52 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N VAL A 40 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N THR A 54 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N LEU A 38 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ARG A 56 " --> pdb=" O TYR A 36 " (cutoff:3.500A) removed outlier: 8.945A pdb=" N GLN A 173 " --> pdb=" O TYR A 36 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LEU A 38 " --> pdb=" O GLN A 173 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N ASP A 175 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N VAL A 40 " --> pdb=" O ASP A 175 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N HIS A 177 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N SER A 42 " --> pdb=" O HIS A 177 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N PHE A 179 " --> pdb=" O SER A 42 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N VAL A 44 " --> pdb=" O PHE A 179 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 94 through 97 removed outlier: 8.885A pdb=" N THR A 589 " --> pdb=" O ALA A 120 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ALA A 120 " --> pdb=" O THR A 589 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET A 591 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LYS A 162 " --> pdb=" O GLU A 72 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 94 through 97 removed outlier: 8.885A pdb=" N THR A 589 " --> pdb=" O ALA A 120 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ALA A 120 " --> pdb=" O THR A 589 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET A 591 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LYS A 162 " --> pdb=" O GLU A 72 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 320 through 321 removed outlier: 3.603A pdb=" N VAL A 327 " --> pdb=" O PHE A 310 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 320 through 321 removed outlier: 6.037A pdb=" N ASN A 274 " --> pdb=" O LEU A 379 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N ILE A 381 " --> pdb=" O ASN A 274 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL A 276 " --> pdb=" O ILE A 381 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N LEU A 383 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL A 278 " --> pdb=" O LEU A 383 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N SER A 378 " --> pdb=" O SER A 411 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N PHE A 413 " --> pdb=" O SER A 378 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ILE A 380 " --> pdb=" O PHE A 413 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N LEU A 415 " --> pdb=" O ILE A 380 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU A 382 " --> pdb=" O LEU A 415 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N PHE A 417 " --> pdb=" O LEU A 382 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N THR A 384 " --> pdb=" O PHE A 417 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N ARG A 438 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N CYS A 414 " --> pdb=" O ARG A 438 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ILE A 440 " --> pdb=" O CYS A 414 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N GLY A 416 " --> pdb=" O ILE A 440 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 2 through 5 removed outlier: 3.561A pdb=" N GLN D 2 " --> pdb=" O SER D 24 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL D 17 " --> pdb=" O LEU D 82 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 9 through 10 removed outlier: 3.689A pdb=" N THR D 112 " --> pdb=" O GLU D 9 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LYS D 37 " --> pdb=" O TRP D 46 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N TRP D 46 " --> pdb=" O LYS D 37 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY D 56 " --> pdb=" O ASP D 51 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 9 through 10 removed outlier: 3.689A pdb=" N THR D 112 " --> pdb=" O GLU D 9 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 122 through 126 removed outlier: 6.053A pdb=" N TYR D 177 " --> pdb=" O GLY D 146 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 122 through 126 removed outlier: 6.053A pdb=" N TYR D 177 " --> pdb=" O GLY D 146 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 153 through 156 Processing sheet with id=AB3, first strand: chain 'E' and resid 5 through 7 Processing sheet with id=AB4, first strand: chain 'E' and resid 53 through 54 removed outlier: 4.071A pdb=" N TYR E 50 " --> pdb=" O THR E 53 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N LEU E 46 " --> pdb=" O GLN E 37 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N GLN E 37 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE E 48 " --> pdb=" O TRP E 35 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N TYR E 50 " --> pdb=" O ILE E 33 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE E 33 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN E 90 " --> pdb=" O THR E 96 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 114 through 116 removed outlier: 3.930A pdb=" N ASN E 137 " --> pdb=" O TYR E 172 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N TYR E 172 " --> pdb=" O ASN E 137 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 152 through 153 341 hydrogen bonds defined for protein. 909 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: 1.14 Time building geometry restraints manager: 0.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2244 1.34 - 1.46: 1713 1.46 - 1.58: 3199 1.58 - 1.70: 0 1.70 - 1.82: 45 Bond restraints: 7201 Sorted by residual: bond pdb=" N SER D 114 " pdb=" CA SER D 114 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.27e-02 6.20e+03 6.46e+00 bond pdb=" N LYS D 117 " pdb=" CA LYS D 117 " ideal model delta sigma weight residual 1.455 1.487 -0.031 1.30e-02 5.92e+03 5.87e+00 bond pdb=" N ALA D 116 " pdb=" CA ALA D 116 " ideal model delta sigma weight residual 1.456 1.485 -0.030 1.25e-02 6.40e+03 5.60e+00 bond pdb=" C LEU A 415 " pdb=" N GLY A 416 " ideal model delta sigma weight residual 1.332 1.343 -0.011 5.00e-03 4.00e+04 4.53e+00 bond pdb=" N THR D 118 " pdb=" CA THR D 118 " ideal model delta sigma weight residual 1.456 1.481 -0.025 1.22e-02 6.72e+03 4.32e+00 ... (remaining 7196 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 9310 1.71 - 3.43: 355 3.43 - 5.14: 73 5.14 - 6.86: 26 6.86 - 8.57: 6 Bond angle restraints: 9770 Sorted by residual: angle pdb=" CB GLU D 61 " pdb=" CG GLU D 61 " pdb=" CD GLU D 61 " ideal model delta sigma weight residual 112.60 120.43 -7.83 1.70e+00 3.46e-01 2.12e+01 angle pdb=" CA GLU D 61 " pdb=" CB GLU D 61 " pdb=" CG GLU D 61 " ideal model delta sigma weight residual 114.10 121.69 -7.59 2.00e+00 2.50e-01 1.44e+01 angle pdb=" CA ARG E 187 " pdb=" CB ARG E 187 " pdb=" CG ARG E 187 " ideal model delta sigma weight residual 114.10 121.47 -7.37 2.00e+00 2.50e-01 1.36e+01 angle pdb=" CA ARG E 107 " pdb=" CB ARG E 107 " pdb=" CG ARG E 107 " ideal model delta sigma weight residual 114.10 121.44 -7.34 2.00e+00 2.50e-01 1.35e+01 angle pdb=" CA THR D 118 " pdb=" CB THR D 118 " pdb=" OG1 THR D 118 " ideal model delta sigma weight residual 109.60 104.93 4.67 1.50e+00 4.44e-01 9.71e+00 ... (remaining 9765 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 3928 17.99 - 35.98: 360 35.98 - 53.97: 78 53.97 - 71.96: 12 71.96 - 89.95: 10 Dihedral angle restraints: 4388 sinusoidal: 1772 harmonic: 2616 Sorted by residual: dihedral pdb=" CA LEU A 347 " pdb=" C LEU A 347 " pdb=" N GLY A 348 " pdb=" CA GLY A 348 " ideal model delta harmonic sigma weight residual -180.00 -156.82 -23.18 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA GLU A 255 " pdb=" C GLU A 255 " pdb=" N ASN A 256 " pdb=" CA ASN A 256 " ideal model delta harmonic sigma weight residual 180.00 158.05 21.95 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA PHE A 315 " pdb=" C PHE A 315 " pdb=" N SER A 316 " pdb=" CA SER A 316 " ideal model delta harmonic sigma weight residual 180.00 160.26 19.74 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 4385 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 886 0.056 - 0.112: 172 0.112 - 0.168: 60 0.168 - 0.224: 2 0.224 - 0.280: 1 Chirality restraints: 1121 Sorted by residual: chirality pdb=" C1 NAG A 701 " pdb=" ND2 ASN A 207 " pdb=" C2 NAG A 701 " pdb=" O5 NAG A 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CA ILE E 48 " pdb=" N ILE E 48 " pdb=" C ILE E 48 " pdb=" CB ILE E 48 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.75e-01 chirality pdb=" CA ILE A 313 " pdb=" N ILE A 313 " pdb=" C ILE A 313 " pdb=" CB ILE A 313 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.08e-01 ... (remaining 1118 not shown) Planarity restraints: 1244 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 185 " 0.012 2.00e-02 2.50e+03 1.85e-02 6.86e+00 pdb=" CG TYR E 185 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TYR E 185 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR E 185 " 0.024 2.00e-02 2.50e+03 pdb=" CE1 TYR E 185 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR E 185 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR E 185 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR E 185 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER E 202 " -0.041 5.00e-02 4.00e+02 6.18e-02 6.10e+00 pdb=" N PRO E 203 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO E 203 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 203 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 586 " 0.040 5.00e-02 4.00e+02 6.01e-02 5.77e+00 pdb=" N PRO A 587 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 587 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 587 " 0.033 5.00e-02 4.00e+02 ... (remaining 1241 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 35 2.67 - 3.22: 6097 3.22 - 3.78: 10008 3.78 - 4.34: 13539 4.34 - 4.90: 23228 Nonbonded interactions: 52907 Sorted by model distance: nonbonded pdb="MG MG A 703 " pdb=" O HOH A 801 " model vdw 2.107 2.170 nonbonded pdb=" OG SER A 284 " pdb="MG MG A 703 " model vdw 2.115 2.170 nonbonded pdb=" OG1 THR A 350 " pdb="MG MG A 703 " model vdw 2.134 2.170 nonbonded pdb="MG MG A 703 " pdb=" O HOH A 802 " model vdw 2.227 2.170 nonbonded pdb=" OG SER A 282 " pdb="MG MG A 703 " model vdw 2.417 2.170 ... (remaining 52902 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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: 0.010 Normalize map: mean=0, sd=1: 0.380 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: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.830 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 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 : 0.005 0.053 7209 Z= 0.216 Angle : 0.858 9.269 9790 Z= 0.446 Chirality : 0.051 0.280 1121 Planarity : 0.006 0.067 1241 Dihedral : 15.185 89.949 2688 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 0.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.02 % Allowed : 17.01 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % 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: -0.43 (0.28), residues: 880 helix: -1.00 (0.40), residues: 148 sheet: 0.77 (0.27), residues: 384 loop : -1.11 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 187 TYR 0.043 0.002 TYR E 185 PHE 0.021 0.002 PHE A 425 TRP 0.009 0.001 TRP D 46 HIS 0.005 0.001 HIS A 441 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.22 ( 7201) covalent geometry : angle 0.85137 / 0.44 ( 9770) SS BOND : bond 0.00875 / 0.44 ( 4) SS BOND : angle 0.99776 / 0.47 ( 8) hydrogen bonds : bond 0.12320 / 8.40 ( 295) hydrogen bonds : angle 6.15386 / 4.28 ( 909) link_BETA1-4 : bond 0.01824 / 0.96 ( 1) link_BETA1-4 : angle 5.57455 / 2.93 ( 3) link_NAG-ASN : bond 0.00501 / 0.26 ( 3) link_NAG-ASN : angle 1.64142 / 0.72 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.222 Fit side-chains revert: symmetry clash REVERT: A 33 ILE cc_start: 0.9154 (mm) cc_final: 0.8945 (mm) REVERT: A 84 MET cc_start: 0.7505 (mtt) cc_final: 0.6839 (ttm) REVERT: A 89 MET cc_start: 0.8465 (mmm) cc_final: 0.7984 (mmm) REVERT: A 126 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8538 (pt0) REVERT: D 98 ASP cc_start: 0.8346 (t0) cc_final: 0.8032 (t0) REVERT: E 104 GLU cc_start: 0.7097 (tm-30) cc_final: 0.6570 (tm-30) REVERT: E 107 ARG cc_start: 0.7406 (tpt90) cc_final: 0.7088 (mmm160) REVERT: E 148 LYS cc_start: 0.7486 (mmtm) cc_final: 0.7056 (ttpt) REVERT: E 165 GLN cc_start: 0.7493 (tt0) cc_final: 0.7237 (mt0) REVERT: E 194 GLU cc_start: 0.6931 (tt0) cc_final: 0.6641 (pt0) outliers start: 8 outliers final: 5 residues processed: 99 average time/residue: 0.0737 time to fit residues: 10.3277 Evaluate side-chains 73 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 68 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain E residue 132 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: [49, 53, 5, 33, 65, 62, 51, 38, 61, 45, 74] chunk 49 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 212 HIS ** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.094279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.073735 restraints weight = 17233.128| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 3.89 r_work: 0.3057 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 7209 Z= 0.208 Angle : 0.649 7.706 9790 Z= 0.338 Chirality : 0.045 0.183 1121 Planarity : 0.005 0.051 1241 Dihedral : 6.117 55.229 1049 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.20 % Allowed : 17.65 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % 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: -0.03 (0.29), residues: 880 helix: 0.14 (0.42), residues: 149 sheet: 0.87 (0.27), residues: 389 loop : -1.11 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 214 TYR 0.021 0.002 TYR D 49 PHE 0.015 0.002 PHE A 425 TRP 0.013 0.002 TRP D 190 HIS 0.016 0.002 HIS A 212 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.21 ( 7201) covalent geometry : angle 0.64612 / 0.34 ( 9770) SS BOND : bond 0.00701 / 0.35 ( 4) SS BOND : angle 1.28800 / 0.56 ( 8) hydrogen bonds : bond 0.04117 / 2.91 ( 295) hydrogen bonds : angle 5.24658 / 3.72 ( 909) link_BETA1-4 : bond 0.00960 / 0.51 ( 1) link_BETA1-4 : angle 1.50009 / 0.79 ( 3) link_NAG-ASN : bond 0.00195 / 0.10 ( 3) link_NAG-ASN : angle 1.45928 / 0.62 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 58 time to evaluate : 0.304 Fit side-chains REVERT: A 75 LYS cc_start: 0.9128 (pttt) cc_final: 0.8818 (ptpp) REVERT: A 89 MET cc_start: 0.8701 (mmm) cc_final: 0.7949 (mmm) REVERT: A 285 MET cc_start: 0.8587 (mtp) cc_final: 0.8196 (mtp) REVERT: D 98 ASP cc_start: 0.8650 (t0) cc_final: 0.8371 (t0) REVERT: D 213 GLU cc_start: 0.8307 (mp0) cc_final: 0.7967 (mp0) REVERT: E 3 GLN cc_start: 0.8339 (mp10) cc_final: 0.7634 (mp10) REVERT: E 104 GLU cc_start: 0.7328 (tm-30) cc_final: 0.6345 (tm-30) REVERT: E 148 LYS cc_start: 0.7632 (mmtm) cc_final: 0.6672 (ttpt) REVERT: E 165 GLN cc_start: 0.7692 (tt0) cc_final: 0.7446 (mt0) REVERT: E 194 GLU cc_start: 0.6693 (tt0) cc_final: 0.6190 (pt0) outliers start: 25 outliers final: 17 residues processed: 76 average time/residue: 0.0723 time to fit residues: 8.0444 Evaluate side-chains 68 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 51 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 19 MET Chi-restraints excluded: chain D residue 179 MET Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 205 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: [49, 71, 36, 88, 85, 24, 26, 8, 48, 23, 6] chunk 49 optimal weight: 8.9990 chunk 71 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 88 optimal weight: 9.9990 chunk 85 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 433 ASN E 77 ASN E 197 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.093924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.073529 restraints weight = 17040.029| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 3.86 r_work: 0.3054 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7209 Z= 0.158 Angle : 0.578 8.030 9790 Z= 0.300 Chirality : 0.044 0.178 1121 Planarity : 0.004 0.047 1241 Dihedral : 5.797 54.212 1049 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.20 % Allowed : 17.90 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % 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: 0.29 (0.29), residues: 880 helix: 0.84 (0.43), residues: 149 sheet: 1.00 (0.28), residues: 379 loop : -0.99 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 123 TYR 0.018 0.002 TYR D 49 PHE 0.013 0.002 PHE A 142 TRP 0.011 0.002 TRP D 190 HIS 0.004 0.001 HIS D 166 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 ( 7201) covalent geometry : angle 0.57551 / 0.30 ( 9770) SS BOND : bond 0.00614 / 0.31 ( 4) SS BOND : angle 1.02812 / 0.46 ( 8) hydrogen bonds : bond 0.03633 / 2.59 ( 295) hydrogen bonds : angle 4.98409 / 3.53 ( 909) link_BETA1-4 : bond 0.00784 / 0.41 ( 1) link_BETA1-4 : angle 1.77485 / 0.93 ( 3) link_NAG-ASN : bond 0.00131 / 0.07 ( 3) link_NAG-ASN : angle 1.51190 / 0.65 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 60 time to evaluate : 0.282 Fit side-chains REVERT: A 75 LYS cc_start: 0.9127 (pttt) cc_final: 0.8843 (ptpp) REVERT: A 89 MET cc_start: 0.8650 (mmm) cc_final: 0.8091 (mmm) REVERT: D 153 THR cc_start: 0.6932 (OUTLIER) cc_final: 0.6184 (p) REVERT: E 3 GLN cc_start: 0.8413 (mp10) cc_final: 0.7723 (mp10) REVERT: E 104 GLU cc_start: 0.7602 (tm-30) cc_final: 0.6391 (tm-30) REVERT: E 148 LYS cc_start: 0.7426 (mmtm) cc_final: 0.6807 (ttpt) REVERT: E 194 GLU cc_start: 0.6743 (tt0) cc_final: 0.6339 (pt0) outliers start: 25 outliers final: 15 residues processed: 81 average time/residue: 0.0607 time to fit residues: 7.4522 Evaluate side-chains 64 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 48 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 19 MET Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 207 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: [51, 38, 79, 33, 2, 46, 23, 42, 59, 45, 57] chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 = 0.3549 r_free = 0.3549 target = 0.092958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.072532 restraints weight = 17132.826| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 3.85 r_work: 0.3033 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7209 Z= 0.178 Angle : 0.600 11.796 9790 Z= 0.306 Chirality : 0.044 0.157 1121 Planarity : 0.004 0.044 1241 Dihedral : 5.782 55.113 1049 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.45 % Allowed : 19.05 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % 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: 0.30 (0.29), residues: 880 helix: 1.15 (0.44), residues: 150 sheet: 0.97 (0.27), residues: 383 loop : -1.13 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 546 TYR 0.020 0.002 TYR D 49 PHE 0.013 0.002 PHE A 425 TRP 0.009 0.001 TRP D 35 HIS 0.004 0.001 HIS E 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.18 ( 7201) covalent geometry : angle 0.59736 / 0.31 ( 9770) SS BOND : bond 0.00637 / 0.32 ( 4) SS BOND : angle 1.09615 / 0.50 ( 8) hydrogen bonds : bond 0.03657 / 2.59 ( 295) hydrogen bonds : angle 4.95194 / 3.51 ( 909) link_BETA1-4 : bond 0.00644 / 0.34 ( 1) link_BETA1-4 : angle 1.43540 / 0.76 ( 3) link_NAG-ASN : bond 0.00097 / 0.05 ( 3) link_NAG-ASN : angle 1.43520 / 0.61 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 47 time to evaluate : 0.281 Fit side-chains REVERT: A 75 LYS cc_start: 0.9181 (pttt) cc_final: 0.8955 (ptpp) REVERT: A 89 MET cc_start: 0.8611 (mmm) cc_final: 0.8060 (mmm) REVERT: E 3 GLN cc_start: 0.8505 (mp10) cc_final: 0.7806 (mp10) REVERT: E 148 LYS cc_start: 0.7476 (mmtm) cc_final: 0.7104 (tttp) REVERT: E 194 GLU cc_start: 0.6812 (OUTLIER) cc_final: 0.6384 (pt0) outliers start: 27 outliers final: 19 residues processed: 69 average time/residue: 0.0596 time to fit residues: 6.3068 Evaluate side-chains 65 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 45 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 19 MET Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 174 MET Chi-restraints excluded: chain E residue 194 GLU Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 207 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: [83, 31, 52, 43, 40, 36, 26, 79, 27, 48, 15] chunk 83 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 27 optimal weight: 0.4980 chunk 48 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 201 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.091581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.071137 restraints weight = 17186.977| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 3.85 r_work: 0.3004 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 7209 Z= 0.219 Angle : 0.631 9.383 9790 Z= 0.325 Chirality : 0.045 0.172 1121 Planarity : 0.004 0.041 1241 Dihedral : 5.988 55.760 1048 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.96 % Allowed : 19.69 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % 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: 0.31 (0.29), residues: 880 helix: 1.22 (0.43), residues: 150 sheet: 0.98 (0.27), residues: 381 loop : -1.15 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 152 TYR 0.023 0.002 TYR D 49 PHE 0.016 0.002 PHE A 425 TRP 0.010 0.002 TRP D 35 HIS 0.005 0.001 HIS A 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.22 ( 7201) covalent geometry : angle 0.62864 / 0.32 ( 9770) SS BOND : bond 0.00674 / 0.34 ( 4) SS BOND : angle 1.19671 / 0.54 ( 8) hydrogen bonds : bond 0.03987 / 2.82 ( 295) hydrogen bonds : angle 4.96722 / 3.51 ( 909) link_BETA1-4 : bond 0.00550 / 0.29 ( 1) link_BETA1-4 : angle 1.36439 / 0.72 ( 3) link_NAG-ASN : bond 0.00099 / 0.05 ( 3) link_NAG-ASN : angle 1.60809 / 0.69 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 49 time to evaluate : 0.291 Fit side-chains REVERT: A 75 LYS cc_start: 0.9231 (pttt) cc_final: 0.8962 (ptpp) REVERT: A 171 HIS cc_start: 0.7162 (t-90) cc_final: 0.6907 (t-170) REVERT: A 404 GLU cc_start: 0.9096 (OUTLIER) cc_final: 0.8757 (pp20) REVERT: A 410 TYR cc_start: 0.9106 (OUTLIER) cc_final: 0.8119 (m-10) REVERT: D 9 GLU cc_start: 0.7308 (mp0) cc_final: 0.6901 (mp0) REVERT: D 153 THR cc_start: 0.6991 (OUTLIER) cc_final: 0.6252 (p) REVERT: E 3 GLN cc_start: 0.8469 (mp10) cc_final: 0.7774 (mp10) REVERT: E 148 LYS cc_start: 0.7508 (mmtm) cc_final: 0.6891 (ttpt) REVERT: E 194 GLU cc_start: 0.6573 (OUTLIER) cc_final: 0.6010 (pt0) outliers start: 31 outliers final: 22 residues processed: 76 average time/residue: 0.0585 time to fit residues: 6.8480 Evaluate side-chains 74 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 48 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 410 TYR Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 19 MET Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 194 GLU Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 207 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: [53, 5, 79, 24, 6, 47, 36, 42, 58, 75, 2] chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 79 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- 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 = 0.3549 r_free = 0.3549 target = 0.093008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.072571 restraints weight = 16999.814| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 3.87 r_work: 0.3038 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7209 Z= 0.141 Angle : 0.572 9.417 9790 Z= 0.292 Chirality : 0.044 0.165 1121 Planarity : 0.004 0.043 1241 Dihedral : 5.662 54.205 1048 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.45 % Allowed : 20.20 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % 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: 0.43 (0.29), residues: 880 helix: 1.30 (0.43), residues: 150 sheet: 1.06 (0.28), residues: 379 loop : -1.06 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 107 TYR 0.016 0.001 TYR D 49 PHE 0.013 0.001 PHE A 142 TRP 0.009 0.001 TRP D 35 HIS 0.002 0.001 HIS D 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 7201) covalent geometry : angle 0.56936 / 0.29 ( 9770) SS BOND : bond 0.00581 / 0.29 ( 4) SS BOND : angle 0.95882 / 0.44 ( 8) hydrogen bonds : bond 0.03315 / 2.35 ( 295) hydrogen bonds : angle 4.79250 / 3.39 ( 909) link_BETA1-4 : bond 0.00528 / 0.28 ( 1) link_BETA1-4 : angle 1.41903 / 0.75 ( 3) link_NAG-ASN : bond 0.00168 / 0.08 ( 3) link_NAG-ASN : angle 1.58361 / 0.68 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 53 time to evaluate : 0.274 Fit side-chains REVERT: A 75 LYS cc_start: 0.9182 (pttt) cc_final: 0.8913 (ptpp) REVERT: A 171 HIS cc_start: 0.7130 (t-90) cc_final: 0.6879 (t-170) REVERT: A 404 GLU cc_start: 0.9077 (OUTLIER) cc_final: 0.8742 (pp20) REVERT: D 9 GLU cc_start: 0.7242 (mp0) cc_final: 0.6827 (mp0) REVERT: D 153 THR cc_start: 0.7111 (OUTLIER) cc_final: 0.6345 (p) REVERT: D 213 GLU cc_start: 0.8461 (mp0) cc_final: 0.8190 (mp0) REVERT: E 3 GLN cc_start: 0.8425 (mp10) cc_final: 0.7713 (mp10) REVERT: E 148 LYS cc_start: 0.7359 (mmtm) cc_final: 0.6988 (tttp) REVERT: E 194 GLU cc_start: 0.6658 (tt0) cc_final: 0.6049 (pt0) outliers start: 27 outliers final: 20 residues processed: 78 average time/residue: 0.0566 time to fit residues: 6.7519 Evaluate side-chains 72 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 50 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 19 MET Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain D residue 197 CYS Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 120 SER Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 207 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: [31, 28, 58, 8, 68, 75, 17, 9, 73, 63, 66] chunk 31 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 68 optimal weight: 0.4980 chunk 75 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 = 0.3545 r_free = 0.3545 target = 0.092763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.072407 restraints weight = 17116.067| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 3.85 r_work: 0.3042 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 7209 Z= 0.152 Angle : 0.576 9.280 9790 Z= 0.293 Chirality : 0.043 0.167 1121 Planarity : 0.004 0.042 1241 Dihedral : 5.554 54.659 1046 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.20 % Allowed : 20.46 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % 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 (0.29), residues: 880 helix: 1.38 (0.43), residues: 150 sheet: 1.07 (0.28), residues: 379 loop : -1.04 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 187 TYR 0.020 0.001 TYR E 185 PHE 0.012 0.001 PHE A 425 TRP 0.012 0.001 TRP D 156 HIS 0.003 0.001 HIS E 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 ( 7201) covalent geometry : angle 0.57381 / 0.29 ( 9770) SS BOND : bond 0.00557 / 0.28 ( 4) SS BOND : angle 0.98595 / 0.44 ( 8) hydrogen bonds : bond 0.03373 / 2.38 ( 295) hydrogen bonds : angle 4.73865 / 3.35 ( 909) link_BETA1-4 : bond 0.00687 / 0.36 ( 1) link_BETA1-4 : angle 1.44103 / 0.76 ( 3) link_NAG-ASN : bond 0.00142 / 0.07 ( 3) link_NAG-ASN : angle 1.56726 / 0.68 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 52 time to evaluate : 0.273 Fit side-chains REVERT: A 75 LYS cc_start: 0.9177 (pttt) cc_final: 0.8923 (ptpp) REVERT: A 171 HIS cc_start: 0.7200 (t-90) cc_final: 0.6931 (t-170) REVERT: A 404 GLU cc_start: 0.9081 (OUTLIER) cc_final: 0.8756 (pp20) REVERT: D 9 GLU cc_start: 0.7257 (mp0) cc_final: 0.6826 (mp0) REVERT: D 153 THR cc_start: 0.7146 (OUTLIER) cc_final: 0.6370 (p) REVERT: E 3 GLN cc_start: 0.8446 (mp10) cc_final: 0.7724 (mp10) REVERT: E 148 LYS cc_start: 0.7386 (mmtm) cc_final: 0.6820 (ttpt) REVERT: E 194 GLU cc_start: 0.6679 (tt0) cc_final: 0.6067 (pt0) outliers start: 25 outliers final: 22 residues processed: 75 average time/residue: 0.0585 time to fit residues: 6.7213 Evaluate side-chains 72 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 48 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 365 SER Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 19 MET Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain D residue 197 CYS Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 207 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: [42, 22, 67, 35, 75, 44, 3, 46, 59, 38, 82] chunk 42 optimal weight: 0.6980 chunk 22 optimal weight: 5.9990 chunk 67 optimal weight: 0.0040 chunk 35 optimal weight: 8.9990 chunk 75 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 82 optimal weight: 0.6980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 173 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.095534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.075815 restraints weight = 16852.078| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 3.74 r_work: 0.3110 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.4018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7209 Z= 0.102 Angle : 0.548 9.136 9790 Z= 0.277 Chirality : 0.043 0.163 1121 Planarity : 0.004 0.044 1241 Dihedral : 5.228 53.091 1046 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.81 % Allowed : 21.10 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % 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: 0.58 (0.29), residues: 880 helix: 1.50 (0.44), residues: 148 sheet: 1.11 (0.28), residues: 381 loop : -0.93 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 107 TYR 0.018 0.001 TYR E 185 PHE 0.010 0.001 PHE A 142 TRP 0.009 0.001 TRP E 35 HIS 0.002 0.001 HIS D 34 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 ( 7201) covalent geometry : angle 0.54496 / 0.28 ( 9770) SS BOND : bond 0.00428 / 0.22 ( 4) SS BOND : angle 0.70006 / 0.32 ( 8) hydrogen bonds : bond 0.02790 / 1.96 ( 295) hydrogen bonds : angle 4.54884 / 3.23 ( 909) link_BETA1-4 : bond 0.00806 / 0.42 ( 1) link_BETA1-4 : angle 1.58797 / 0.83 ( 3) link_NAG-ASN : bond 0.00279 / 0.14 ( 3) link_NAG-ASN : angle 1.59718 / 0.70 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 54 time to evaluate : 0.291 Fit side-chains REVERT: A 75 LYS cc_start: 0.9101 (pttt) cc_final: 0.8892 (ptpp) REVERT: A 404 GLU cc_start: 0.9024 (OUTLIER) cc_final: 0.8750 (pp20) REVERT: D 9 GLU cc_start: 0.7321 (mp0) cc_final: 0.6844 (mp0) REVERT: D 153 THR cc_start: 0.7443 (OUTLIER) cc_final: 0.6675 (p) REVERT: D 185 VAL cc_start: 0.7463 (t) cc_final: 0.6955 (p) REVERT: D 213 GLU cc_start: 0.8395 (mp0) cc_final: 0.8097 (mp0) REVERT: E 3 GLN cc_start: 0.8536 (mp10) cc_final: 0.7814 (mp10) REVERT: E 148 LYS cc_start: 0.7356 (mmtm) cc_final: 0.7015 (tttp) REVERT: E 184 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7293 (pp20) REVERT: E 194 GLU cc_start: 0.6939 (tt0) cc_final: 0.6724 (pt0) outliers start: 22 outliers final: 13 residues processed: 74 average time/residue: 0.0630 time to fit residues: 7.0884 Evaluate side-chains 68 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 52 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain D residue 197 CYS Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 184 GLU Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 207 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: [36, 27, 35, 8, 74, 26, 4, 30, 51, 52, 18] chunk 36 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 171 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.095707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.075860 restraints weight = 16882.494| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 3.76 r_work: 0.3114 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.4045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7209 Z= 0.104 Angle : 0.555 9.046 9790 Z= 0.281 Chirality : 0.043 0.160 1121 Planarity : 0.003 0.044 1241 Dihedral : 5.161 53.599 1046 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.56 % Allowed : 21.23 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % 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: 0.70 (0.29), residues: 880 helix: 1.46 (0.44), residues: 150 sheet: 1.21 (0.28), residues: 378 loop : -0.83 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 107 TYR 0.017 0.001 TYR E 185 PHE 0.010 0.001 PHE E 134 TRP 0.009 0.001 TRP E 35 HIS 0.003 0.001 HIS E 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 ( 7201) covalent geometry : angle 0.55263 / 0.28 ( 9770) SS BOND : bond 0.00436 / 0.22 ( 4) SS BOND : angle 0.74883 / 0.34 ( 8) hydrogen bonds : bond 0.02785 / 1.97 ( 295) hydrogen bonds : angle 4.46645 / 3.17 ( 909) link_BETA1-4 : bond 0.00759 / 0.40 ( 1) link_BETA1-4 : angle 1.50611 / 0.79 ( 3) link_NAG-ASN : bond 0.00269 / 0.13 ( 3) link_NAG-ASN : angle 1.67246 / 0.73 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 53 time to evaluate : 0.182 Fit side-chains REVERT: A 75 LYS cc_start: 0.9098 (pttt) cc_final: 0.8897 (ptpp) REVERT: A 404 GLU cc_start: 0.9013 (OUTLIER) cc_final: 0.8752 (pp20) REVERT: D 2 GLN cc_start: 0.7943 (pm20) cc_final: 0.7643 (pm20) REVERT: D 9 GLU cc_start: 0.7318 (mp0) cc_final: 0.6838 (mp0) REVERT: D 153 THR cc_start: 0.7450 (OUTLIER) cc_final: 0.6683 (p) REVERT: D 185 VAL cc_start: 0.7612 (t) cc_final: 0.7233 (p) REVERT: D 213 GLU cc_start: 0.8203 (mp0) cc_final: 0.7893 (mp0) REVERT: E 3 GLN cc_start: 0.8551 (mp10) cc_final: 0.7824 (mp10) REVERT: E 148 LYS cc_start: 0.7368 (mmtm) cc_final: 0.7036 (tttp) REVERT: E 184 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.7247 (pp20) REVERT: E 194 GLU cc_start: 0.6950 (tt0) cc_final: 0.6747 (pt0) outliers start: 20 outliers final: 16 residues processed: 70 average time/residue: 0.0606 time to fit residues: 6.4641 Evaluate side-chains 71 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 52 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 19 MET Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain D residue 197 CYS Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 177 THR Chi-restraints excluded: chain E residue 184 GLU Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 207 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: [24, 65, 54, 33, 41, 28, 23, 5, 35, 86, 72] chunk 24 optimal weight: 7.9990 chunk 65 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 chunk 72 optimal weight: 0.0020 overall best weight: 0.8790 ------------------------------------------------------------------------------- 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 = 0.3595 r_free = 0.3595 target = 0.095295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.075458 restraints weight = 16766.218| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 3.74 r_work: 0.3106 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7209 Z= 0.113 Angle : 0.556 8.964 9790 Z= 0.282 Chirality : 0.043 0.155 1121 Planarity : 0.003 0.044 1241 Dihedral : 5.130 53.942 1045 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.30 % Allowed : 21.36 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % 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: 0.68 (0.29), residues: 880 helix: 1.49 (0.44), residues: 150 sheet: 1.20 (0.27), residues: 379 loop : -0.88 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 56 TYR 0.018 0.001 TYR E 185 PHE 0.010 0.001 PHE A 142 TRP 0.009 0.001 TRP E 35 HIS 0.003 0.001 HIS E 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 ( 7201) covalent geometry : angle 0.55335 / 0.28 ( 9770) SS BOND : bond 0.00475 / 0.24 ( 4) SS BOND : angle 0.83109 / 0.38 ( 8) hydrogen bonds : bond 0.02875 / 2.02 ( 295) hydrogen bonds : angle 4.45971 / 3.17 ( 909) link_BETA1-4 : bond 0.00701 / 0.37 ( 1) link_BETA1-4 : angle 1.42208 / 0.75 ( 3) link_NAG-ASN : bond 0.00216 / 0.10 ( 3) link_NAG-ASN : angle 1.70066 / 0.74 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1760 Ramachandran restraints generated. 880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 52 time to evaluate : 0.194 Fit side-chains REVERT: A 404 GLU cc_start: 0.9008 (OUTLIER) cc_final: 0.8754 (pp20) REVERT: D 2 GLN cc_start: 0.7944 (pm20) cc_final: 0.7637 (pm20) REVERT: D 9 GLU cc_start: 0.7328 (mp0) cc_final: 0.6848 (mp0) REVERT: D 153 THR cc_start: 0.7439 (OUTLIER) cc_final: 0.6670 (p) REVERT: D 185 VAL cc_start: 0.7599 (t) cc_final: 0.7210 (p) REVERT: D 193 GLN cc_start: 0.7914 (tp40) cc_final: 0.7452 (tm-30) REVERT: D 213 GLU cc_start: 0.8210 (mp0) cc_final: 0.7905 (mp0) REVERT: E 3 GLN cc_start: 0.8560 (mp10) cc_final: 0.7833 (mp10) REVERT: E 148 LYS cc_start: 0.7377 (mmtm) cc_final: 0.7019 (tttp) REVERT: E 194 GLU cc_start: 0.6950 (tt0) cc_final: 0.6723 (pt0) outliers start: 18 outliers final: 13 residues processed: 69 average time/residue: 0.0645 time to fit residues: 6.7180 Evaluate side-chains 65 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 50 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain D residue 17 VAL Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 189 THR Chi-restraints excluded: chain D residue 197 CYS Chi-restraints excluded: chain E residue 89 LEU Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 207 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: [31, 57, 25, 81, 5, 87, 42, 18, 8, 59, 84] chunk 31 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 42 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 70.3399 > 50:) chunk 18 optimal weight: 0.0770 chunk 8 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 overall best weight: 1.2146 ------------------------------------------------------------------------------- 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 = 0.3587 r_free = 0.3587 target = 0.094684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.074706 restraints weight = 16767.498| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 3.77 r_work: 0.3092 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.4179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7209 Z= 0.133 Angle : 0.565 9.232 9790 Z= 0.286 Chirality : 0.043 0.156 1121 Planarity : 0.003 0.043 1241 Dihedral : 5.224 54.380 1045 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.30 % Allowed : 21.61 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % 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 (0.29), residues: 880 helix: 1.49 (0.44), residues: 150 sheet: 1.18 (0.27), residues: 380 loop : -0.93 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 338 TYR 0.018 0.001 TYR E 185 PHE 0.011 0.001 PHE A 142 TRP 0.008 0.001 TRP D 46 HIS 0.003 0.001 HIS E 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 7201) covalent geometry : angle 0.56180 / 0.29 ( 9770) SS BOND : bond 0.00525 / 0.26 ( 4) SS BOND : angle 0.92267 / 0.42 ( 8) hydrogen bonds : bond 0.03098 / 2.17 ( 295) hydrogen bonds : angle 4.52019 / 3.20 ( 909) link_BETA1-4 : bond 0.00595 / 0.31 ( 1) link_BETA1-4 : angle 1.32370 / 0.70 ( 3) link_NAG-ASN : bond 0.00188 / 0.09 ( 3) link_NAG-ASN : angle 1.66120 / 0.72 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1507.64 seconds wall clock time: 26 minutes 42.79 seconds (1602.79 seconds total)