Starting phenix.real_space_refine on Fri Oct 23 01:13:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m8e_63708/10_2026/9m8e_63708.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m8e_63708/10_2026/9m8e_63708.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9m8e_63708/10_2026/9m8e_63708.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m8e_63708/10_2026/9m8e_63708.map" model { file = "/net/cci-nas-00/data/ceres_data/9m8e_63708/10_2026/9m8e_63708.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m8e_63708/10_2026/9m8e_63708.cif" } resolution = 2.53 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.086 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 P 4 5.49 5 S 22 5.16 5 C 4604 2.51 5 N 1260 2.21 5 O 1406 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 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: 7296 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 283 Classifications: {'peptide': 41} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 39} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 3449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3449 Classifications: {'peptide': 462} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 447} Chain: "A" Number of atoms: 3458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3458 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 449} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.64, per 1000 atoms: 0.22 Number of scatterers: 7296 At special positions: 0 Unit cell: (86.1, 90.2, 111.52, 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 22 16.00 P 4 15.00 O 1406 8.00 N 1260 7.00 C 4604 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 46 " distance=2.03 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 46 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.61 Conformation dependent library (CDL) restraints added in 424.3 milliseconds 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1724 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 14 sheets defined 41.7% alpha, 25.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'C' and resid 245 through 255 removed outlier: 3.770A pdb=" N SER C 253 " --> pdb=" O ARG C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 283 removed outlier: 3.517A pdb=" N LYS C 283 " --> pdb=" O ALA C 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 25 Processing helix chain 'B' and resid 38 through 44 Processing helix chain 'B' and resid 45 through 65 Processing helix chain 'B' and resid 78 through 104 removed outlier: 3.869A pdb=" N ALA B 82 " --> pdb=" O ASP B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 166 Processing helix chain 'B' and resid 180 through 193 Processing helix chain 'B' and resid 211 through 226 Processing helix chain 'B' and resid 277 through 282 removed outlier: 3.588A pdb=" N ALA B 281 " --> pdb=" O GLY B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 312 Processing helix chain 'B' and resid 316 through 333 Processing helix chain 'B' and resid 341 through 345 removed outlier: 3.514A pdb=" N LEU B 345 " --> pdb=" O HIS B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 368 Processing helix chain 'B' and resid 382 through 389 Processing helix chain 'B' and resid 415 through 418 removed outlier: 3.678A pdb=" N GLU B 418 " --> pdb=" O ASP B 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 415 through 418' Processing helix chain 'B' and resid 419 through 429 removed outlier: 4.579A pdb=" N LEU B 423 " --> pdb=" O LEU B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 437 Processing helix chain 'B' and resid 447 through 459 Processing helix chain 'A' and resid 12 through 25 removed outlier: 3.621A pdb=" N VAL A 17 " --> pdb=" O PRO A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 45 removed outlier: 3.553A pdb=" N LEU A 42 " --> pdb=" O GLY A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 70 removed outlier: 3.536A pdb=" N SER A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N LYS A 67 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ALA A 68 " --> pdb=" O LYS A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 104 removed outlier: 3.762A pdb=" N ALA A 82 " --> pdb=" O ASP A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 166 Processing helix chain 'A' and resid 180 through 193 Processing helix chain 'A' and resid 211 through 226 Processing helix chain 'A' and resid 308 through 312 removed outlier: 3.563A pdb=" N ASN A 311 " --> pdb=" O GLY A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 333 Processing helix chain 'A' and resid 341 through 345 removed outlier: 3.524A pdb=" N MET A 344 " --> pdb=" O ASP A 341 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A 345 " --> pdb=" O HIS A 342 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 341 through 345' Processing helix chain 'A' and resid 361 through 368 Processing helix chain 'A' and resid 382 through 389 Processing helix chain 'A' and resid 415 through 418 removed outlier: 3.655A pdb=" N GLU A 418 " --> pdb=" O ASP A 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 415 through 418' Processing helix chain 'A' and resid 419 through 429 removed outlier: 4.528A pdb=" N LEU A 423 " --> pdb=" O LEU A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 437 Processing helix chain 'A' and resid 447 through 459 removed outlier: 3.588A pdb=" N GLN A 451 " --> pdb=" O SER A 447 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 107 through 109 removed outlier: 6.673A pdb=" N THR B 29 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N ILE B 109 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ILE B 31 " --> pdb=" O ILE B 109 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N THR B 2 " --> pdb=" O THR B 134 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N ASP B 136 " --> pdb=" O THR B 2 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N TYR B 4 " --> pdb=" O ASP B 136 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N ALA B 138 " --> pdb=" O TYR B 4 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N VAL B 6 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 10.127A pdb=" N ILE B 140 " --> pdb=" O VAL B 6 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N VAL B 8 " --> pdb=" O ILE B 140 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 107 through 109 removed outlier: 6.673A pdb=" N THR B 29 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N ILE B 109 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ILE B 31 " --> pdb=" O ILE B 109 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N THR B 2 " --> pdb=" O THR B 134 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N ASP B 136 " --> pdb=" O THR B 2 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N TYR B 4 " --> pdb=" O ASP B 136 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N ALA B 138 " --> pdb=" O TYR B 4 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N VAL B 6 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 10.127A pdb=" N ILE B 140 " --> pdb=" O VAL B 6 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N VAL B 8 " --> pdb=" O ILE B 140 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'B' and resid 76 through 77 Processing sheet with id=AA5, first strand: chain 'B' and resid 144 through 146 Processing sheet with id=AA6, first strand: chain 'B' and resid 158 through 159 Processing sheet with id=AA7, first strand: chain 'B' and resid 234 through 241 removed outlier: 5.887A pdb=" N VAL B 235 " --> pdb=" O THR B 250 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N THR B 250 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER B 237 " --> pdb=" O THR B 248 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL B 249 " --> pdb=" O GLN B 256 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 347 through 349 removed outlier: 6.757A pdb=" N VAL B 398 " --> pdb=" O LEU B 407 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N GLY B 409 " --> pdb=" O LYS B 396 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LYS B 396 " --> pdb=" O GLY B 409 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LEU B 411 " --> pdb=" O PHE B 394 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N PHE B 394 " --> pdb=" O LEU B 411 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 107 through 109 removed outlier: 6.989A pdb=" N THR A 29 " --> pdb=" O THR A 107 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N ILE A 109 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ILE A 31 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N THR A 2 " --> pdb=" O THR A 134 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N ASP A 136 " --> pdb=" O THR A 2 " (cutoff:3.500A) removed outlier: 9.002A pdb=" N TYR A 4 " --> pdb=" O ASP A 136 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ALA A 138 " --> pdb=" O TYR A 4 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N VAL A 6 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 10.132A pdb=" N ILE A 140 " --> pdb=" O VAL A 6 " (cutoff:3.500A) removed outlier: 8.923A pdb=" N VAL A 8 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N THR A 120 " --> pdb=" O ALA A 116 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 107 through 109 removed outlier: 6.989A pdb=" N THR A 29 " --> pdb=" O THR A 107 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N ILE A 109 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ILE A 31 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N THR A 2 " --> pdb=" O THR A 134 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N ASP A 136 " --> pdb=" O THR A 2 " (cutoff:3.500A) removed outlier: 9.002A pdb=" N TYR A 4 " --> pdb=" O ASP A 136 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ALA A 138 " --> pdb=" O TYR A 4 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N VAL A 6 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 10.132A pdb=" N ILE A 140 " --> pdb=" O VAL A 6 " (cutoff:3.500A) removed outlier: 8.923A pdb=" N VAL A 8 " --> pdb=" O ILE A 140 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 144 through 146 Processing sheet with id=AB3, first strand: chain 'A' and resid 158 through 159 removed outlier: 6.946A pdb=" N VAL A 197 " --> pdb=" O THR A 228 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N LEU A 230 " --> pdb=" O VAL A 197 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE A 199 " --> pdb=" O LEU A 230 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 233 through 240 removed outlier: 5.669A pdb=" N VAL A 235 " --> pdb=" O THR A 250 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N THR A 250 " --> pdb=" O VAL A 235 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 347 through 349 removed outlier: 6.734A pdb=" N VAL A 398 " --> pdb=" O LEU A 407 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N GLY A 409 " --> pdb=" O LYS A 396 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N LYS A 396 " --> pdb=" O GLY A 409 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N LEU A 411 " --> pdb=" O PHE A 394 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N PHE A 394 " --> pdb=" O LEU A 411 " (cutoff:3.500A) 372 hydrogen bonds defined for protein. 1065 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: 1.27 Time building geometry restraints manager: 0.73 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: 2448 1.34 - 1.46: 1595 1.46 - 1.58: 3345 1.58 - 1.70: 4 1.70 - 1.82: 36 Bond restraints: 7428 Sorted by residual: bond pdb=" O3P FAD B 501 " pdb=" P FAD B 501 " ideal model delta sigma weight residual 1.660 1.581 0.079 2.00e-02 2.50e+03 1.54e+01 bond pdb=" O5B FAD B 501 " pdb=" PA FAD B 501 " ideal model delta sigma weight residual 1.634 1.559 0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" O3P FAD A 501 " pdb=" P FAD A 501 " ideal model delta sigma weight residual 1.660 1.588 0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" O5B FAD A 501 " pdb=" PA FAD A 501 " ideal model delta sigma weight residual 1.634 1.567 0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" O5' FAD B 501 " pdb=" P FAD B 501 " ideal model delta sigma weight residual 1.637 1.575 0.062 2.00e-02 2.50e+03 9.48e+00 ... (remaining 7423 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 9946 1.80 - 3.59: 132 3.59 - 5.39: 18 5.39 - 7.18: 8 7.18 - 8.98: 3 Bond angle restraints: 10107 Sorted by residual: angle pdb=" CA LYS B 216 " pdb=" CB LYS B 216 " pdb=" CG LYS B 216 " ideal model delta sigma weight residual 114.10 121.10 -7.00 2.00e+00 2.50e-01 1.23e+01 angle pdb=" CB LYS B 216 " pdb=" CG LYS B 216 " pdb=" CD LYS B 216 " ideal model delta sigma weight residual 111.30 118.98 -7.68 2.30e+00 1.89e-01 1.12e+01 angle pdb=" O1P FAD A 501 " pdb=" P FAD A 501 " pdb=" O2P FAD A 501 " ideal model delta sigma weight residual 122.50 113.52 8.98 3.00e+00 1.11e-01 8.96e+00 angle pdb=" O1P FAD B 501 " pdb=" P FAD B 501 " pdb=" O2P FAD B 501 " ideal model delta sigma weight residual 122.50 114.39 8.11 3.00e+00 1.11e-01 7.31e+00 angle pdb=" N LEU A 420 " pdb=" CA LEU A 420 " pdb=" C LEU A 420 " ideal model delta sigma weight residual 109.81 115.65 -5.84 2.21e+00 2.05e-01 6.99e+00 ... (remaining 10102 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 3810 17.95 - 35.90: 421 35.90 - 53.85: 145 53.85 - 71.80: 27 71.80 - 89.76: 10 Dihedral angle restraints: 4413 sinusoidal: 1699 harmonic: 2714 Sorted by residual: dihedral pdb=" CB CYS B 41 " pdb=" SG CYS B 41 " pdb=" SG CYS B 46 " pdb=" CB CYS B 46 " ideal model delta sinusoidal sigma weight residual -86.00 -133.35 47.35 1 1.00e+01 1.00e-02 3.10e+01 dihedral pdb=" CB CYS A 41 " pdb=" SG CYS A 41 " pdb=" SG CYS A 46 " pdb=" CB CYS A 46 " ideal model delta sinusoidal sigma weight residual -86.00 -132.86 46.86 1 1.00e+01 1.00e-02 3.04e+01 dihedral pdb=" CB GLU A 108 " pdb=" CG GLU A 108 " pdb=" CD GLU A 108 " pdb=" OE1 GLU A 108 " ideal model delta sinusoidal sigma weight residual 0.00 89.76 -89.76 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 4410 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 747 0.029 - 0.058: 235 0.058 - 0.087: 88 0.087 - 0.116: 98 0.116 - 0.145: 18 Chirality restraints: 1186 Sorted by residual: chirality pdb=" C2B FAD B 501 " pdb=" C1B FAD B 501 " pdb=" C3B FAD B 501 " pdb=" O2B FAD B 501 " both_signs ideal model delta sigma weight residual False -2.53 -2.68 0.15 2.00e-01 2.50e+01 5.29e-01 chirality pdb=" CA VAL B 149 " pdb=" N VAL B 149 " pdb=" C VAL B 149 " pdb=" CB VAL B 149 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.04e-01 chirality pdb=" C2B FAD A 501 " pdb=" C1B FAD A 501 " pdb=" C3B FAD A 501 " pdb=" O2B FAD A 501 " both_signs ideal model delta sigma weight residual False -2.53 -2.68 0.14 2.00e-01 2.50e+01 4.92e-01 ... (remaining 1183 not shown) Planarity restraints: 1293 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 270 " -0.023 5.00e-02 4.00e+02 3.51e-02 1.97e+00 pdb=" N PRO B 271 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 271 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 271 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 12 " -0.023 5.00e-02 4.00e+02 3.44e-02 1.90e+00 pdb=" N PRO A 13 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 13 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 13 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 61 " 0.007 2.00e-02 2.50e+03 1.37e-02 1.88e+00 pdb=" C ILE A 61 " -0.024 2.00e-02 2.50e+03 pdb=" O ILE A 61 " 0.009 2.00e-02 2.50e+03 pdb=" N PHE A 62 " 0.008 2.00e-02 2.50e+03 ... (remaining 1290 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 334 2.73 - 3.27: 6746 3.27 - 3.81: 11956 3.81 - 4.36: 14936 4.36 - 4.90: 25459 Nonbonded interactions: 59431 Sorted by model distance: nonbonded pdb=" O CYS A 351 " pdb=" ND2 ASN A 354 " model vdw 2.187 3.120 nonbonded pdb=" O THR B 442 " pdb=" OG1 THR B 445 " model vdw 2.213 3.040 nonbonded pdb=" O CYS B 351 " pdb=" ND2 ASN B 354 " model vdw 2.232 3.120 nonbonded pdb=" O VAL B 149 " pdb=" OG1 THR B 152 " model vdw 2.317 3.040 nonbonded pdb=" O GLY B 39 " pdb=" ND2 ASN B 43 " model vdw 2.318 3.120 ... (remaining 59426 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 462 or resid 501)) selection = (chain 'B' and (resid 1 through 66 or (resid 67 through 68 and (name N or name C \ A or name C or name O or name CB )) or resid 69 through 501)) } 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: 3.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.310 Find NCS groups from input model: 0.120 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:6.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 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 : 0.004 0.079 7430 Z= 0.183 Angle : 0.556 8.980 10111 Z= 0.282 Chirality : 0.044 0.145 1186 Planarity : 0.003 0.035 1293 Dihedral : 17.517 89.756 2683 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.29 % Favored : 97.61 % Rotamer: Outliers : 1.88 % Allowed : 18.57 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % 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: 0.66 (0.27), residues: 961 helix: 1.40 (0.28), residues: 361 sheet: 1.27 (0.37), residues: 226 loop : -1.07 (0.29), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 168 TYR 0.014 0.001 TYR A 16 PHE 0.008 0.001 PHE A 62 TRP 0.012 0.002 TRP B 37 HIS 0.004 0.001 HIS B 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.18 ( 7428) covalent geometry : angle 0.55539 / 0.28 (10107) SS BOND : bond 0.00347 / 0.18 ( 2) SS BOND : angle 1.06897 / 0.45 ( 4) hydrogen bonds : bond 0.17133 / 12.20 ( 366) hydrogen bonds : angle 6.06768 / 4.30 ( 1065) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 50 time to evaluate : 0.265 Fit side-chains outliers start: 14 outliers final: 12 residues processed: 62 average time/residue: 0.5959 time to fit residues: 39.0700 Evaluate side-chains 61 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 153 SER Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 453 CYS Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 343 ARG Chi-restraints excluded: chain A residue 392 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: [49, 53, 5, 33, 65, 62, 51, 38, 61, 45, 74] chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.4980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3492 r_free = 0.3492 target = 0.125683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.102498 restraints weight = 9378.916| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.62 r_work: 0.3088 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8969 moved from start: 0.0601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7430 Z= 0.120 Angle : 0.531 6.570 10111 Z= 0.283 Chirality : 0.045 0.146 1186 Planarity : 0.004 0.033 1293 Dihedral : 10.370 67.623 1137 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.29 % Favored : 97.61 % Rotamer: Outliers : 2.56 % Allowed : 16.96 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % 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: 0.89 (0.27), residues: 961 helix: 1.75 (0.27), residues: 366 sheet: 1.18 (0.36), residues: 236 loop : -1.07 (0.30), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 343 TYR 0.019 0.001 TYR A 16 PHE 0.008 0.001 PHE A 62 TRP 0.010 0.002 TRP A 429 HIS 0.004 0.001 HIS B 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 ( 7428) covalent geometry : angle 0.53007 / 0.28 (10107) SS BOND : bond 0.00769 / 0.40 ( 2) SS BOND : angle 1.33932 / 0.62 ( 4) hydrogen bonds : bond 0.05206 / 3.56 ( 366) hydrogen bonds : angle 4.67837 / 3.37 ( 1065) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 48 time to evaluate : 0.223 Fit side-chains REVERT: B 163 GLU cc_start: 0.8468 (mp0) cc_final: 0.8117 (mp0) REVERT: A 405 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8176 (mt-10) outliers start: 19 outliers final: 7 residues processed: 63 average time/residue: 0.6015 time to fit residues: 40.0632 Evaluate side-chains 55 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain A residue 343 ARG Chi-restraints excluded: chain A residue 405 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: [80, 93, 89, 82, 85, 53, 40, 14, 2, 26, 81] chunk 80 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 85 optimal weight: 0.1980 chunk 53 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 = 0.3477 r_free = 0.3477 target = 0.124361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.101252 restraints weight = 9285.174| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.61 r_work: 0.3060 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8992 moved from start: 0.0734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7430 Z= 0.136 Angle : 0.539 6.761 10111 Z= 0.287 Chirality : 0.046 0.144 1186 Planarity : 0.004 0.033 1293 Dihedral : 9.903 62.924 1124 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.39 % Favored : 97.50 % Rotamer: Outliers : 2.42 % Allowed : 17.23 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % 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: 0.90 (0.27), residues: 961 helix: 1.83 (0.27), residues: 368 sheet: 1.12 (0.36), residues: 236 loop : -1.12 (0.30), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 21 TYR 0.019 0.002 TYR A 16 PHE 0.007 0.001 PHE A 62 TRP 0.011 0.002 TRP A 429 HIS 0.005 0.001 HIS B 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 7428) covalent geometry : angle 0.53855 / 0.29 (10107) SS BOND : bond 0.00953 / 0.47 ( 2) SS BOND : angle 1.17688 / 0.56 ( 4) hydrogen bonds : bond 0.05513 / 3.75 ( 366) hydrogen bonds : angle 4.55374 / 3.27 ( 1065) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 48 time to evaluate : 0.221 Fit side-chains REVERT: A 343 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.7378 (mtp85) REVERT: A 405 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8194 (mt-10) outliers start: 18 outliers final: 6 residues processed: 62 average time/residue: 0.6147 time to fit residues: 40.2492 Evaluate side-chains 55 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 55 ASN Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain A residue 343 ARG Chi-restraints excluded: chain A residue 405 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: [65, 85, 16, 52, 50, 19, 86, 84, 38, 17, 24] chunk 65 optimal weight: 4.9990 chunk 85 optimal weight: 0.5980 chunk 16 optimal weight: 7.9990 chunk 52 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 24 optimal weight: 0.0980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3501 r_free = 0.3501 target = 0.126465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.103070 restraints weight = 9453.732| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 1.64 r_work: 0.3095 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 moved from start: 0.0813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7430 Z= 0.103 Angle : 0.492 6.797 10111 Z= 0.263 Chirality : 0.044 0.145 1186 Planarity : 0.003 0.032 1293 Dihedral : 9.819 59.563 1123 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.19 % Favored : 97.71 % Rotamer: Outliers : 2.15 % Allowed : 17.63 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % 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 (0.27), residues: 961 helix: 2.07 (0.27), residues: 368 sheet: 1.19 (0.37), residues: 221 loop : -1.06 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 147 TYR 0.017 0.001 TYR A 16 PHE 0.009 0.001 PHE A 62 TRP 0.011 0.002 TRP A 429 HIS 0.004 0.001 HIS B 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 ( 7428) covalent geometry : angle 0.49175 / 0.26 (10107) SS BOND : bond 0.00415 / 0.21 ( 2) SS BOND : angle 0.86540 / 0.35 ( 4) hydrogen bonds : bond 0.04400 / 3.00 ( 366) hydrogen bonds : angle 4.34659 / 3.12 ( 1065) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 51 time to evaluate : 0.282 Fit side-chains REVERT: A 343 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.7460 (mtp85) outliers start: 16 outliers final: 8 residues processed: 62 average time/residue: 0.6392 time to fit residues: 41.8149 Evaluate side-chains 55 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 55 ASN Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain A residue 343 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: [13, 90, 84, 21, 55, 11, 91, 8, 79, 58, 5] chunk 13 optimal weight: 7.9990 chunk 90 optimal weight: 7.9990 chunk 84 optimal weight: 2.9990 chunk 21 optimal weight: 8.9990 chunk 55 optimal weight: 3.9990 chunk 11 optimal weight: 0.2980 chunk 91 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 = 0.3468 r_free = 0.3468 target = 0.123723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.100191 restraints weight = 9362.825| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.63 r_work: 0.3056 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8999 moved from start: 0.0864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7430 Z= 0.151 Angle : 0.551 6.886 10111 Z= 0.294 Chirality : 0.046 0.148 1186 Planarity : 0.004 0.035 1293 Dihedral : 10.057 59.980 1123 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.81 % Favored : 97.09 % Rotamer: Outliers : 2.96 % Allowed : 16.82 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % 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: 0.91 (0.27), residues: 961 helix: 1.95 (0.27), residues: 368 sheet: 1.03 (0.35), residues: 236 loop : -1.17 (0.29), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 21 TYR 0.020 0.002 TYR A 16 PHE 0.006 0.001 PHE A 62 TRP 0.011 0.003 TRP A 37 HIS 0.006 0.001 HIS B 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 7428) covalent geometry : angle 0.55105 / 0.29 (10107) SS BOND : bond 0.00846 / 0.43 ( 2) SS BOND : angle 1.21997 / 0.56 ( 4) hydrogen bonds : bond 0.05767 / 3.91 ( 366) hydrogen bonds : angle 4.46907 / 3.22 ( 1065) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 47 time to evaluate : 0.280 Fit side-chains REVERT: B 47 ILE cc_start: 0.8386 (OUTLIER) cc_final: 0.8085 (mm) REVERT: A 244 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.8097 (pt0) REVERT: A 343 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.7393 (mtp85) outliers start: 22 outliers final: 7 residues processed: 64 average time/residue: 0.6471 time to fit residues: 43.5742 Evaluate side-chains 57 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 55 ASN Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain A residue 244 GLN Chi-restraints excluded: chain A residue 343 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: [25, 83, 24, 90, 74, 87, 36, 3, 51, 30, 82] chunk 25 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 = 0.3477 r_free = 0.3477 target = 0.124446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.100985 restraints weight = 9405.768| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.64 r_work: 0.3078 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8988 moved from start: 0.0892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7430 Z= 0.132 Angle : 0.529 7.085 10111 Z= 0.282 Chirality : 0.045 0.143 1186 Planarity : 0.003 0.033 1293 Dihedral : 9.835 59.669 1123 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.60 % Favored : 97.29 % Rotamer: Outliers : 2.29 % Allowed : 17.63 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % 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: 0.99 (0.27), residues: 961 helix: 2.05 (0.27), residues: 368 sheet: 1.06 (0.36), residues: 236 loop : -1.17 (0.29), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 21 TYR 0.018 0.002 TYR A 16 PHE 0.009 0.001 PHE A 62 TRP 0.012 0.002 TRP A 37 HIS 0.005 0.001 HIS B 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 7428) covalent geometry : angle 0.52862 / 0.28 (10107) SS BOND : bond 0.00764 / 0.38 ( 2) SS BOND : angle 1.10286 / 0.46 ( 4) hydrogen bonds : bond 0.05214 / 3.55 ( 366) hydrogen bonds : angle 4.39993 / 3.18 ( 1065) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 50 time to evaluate : 0.279 Fit side-chains REVERT: B 236 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7379 (pt0) REVERT: B 250 THR cc_start: 0.8554 (m) cc_final: 0.8313 (p) REVERT: A 343 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.7402 (mtp85) outliers start: 17 outliers final: 8 residues processed: 64 average time/residue: 0.6188 time to fit residues: 41.7516 Evaluate side-chains 58 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 55 ASN Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 343 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: [52, 28, 76, 18, 79, 74, 35, 78, 30, 24, 44] chunk 52 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 79 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 78 optimal weight: 0.2980 chunk 30 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 = 0.3477 r_free = 0.3477 target = 0.124417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.100904 restraints weight = 9433.854| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.64 r_work: 0.3075 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8988 moved from start: 0.0917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7430 Z= 0.131 Angle : 0.529 7.138 10111 Z= 0.282 Chirality : 0.045 0.144 1186 Planarity : 0.003 0.033 1293 Dihedral : 9.593 59.739 1123 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.81 % Favored : 97.09 % Rotamer: Outliers : 2.56 % Allowed : 17.63 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % 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: 1.00 (0.27), residues: 961 helix: 2.08 (0.27), residues: 368 sheet: 1.06 (0.35), residues: 236 loop : -1.18 (0.29), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 21 TYR 0.018 0.002 TYR A 16 PHE 0.008 0.001 PHE A 62 TRP 0.012 0.002 TRP A 37 HIS 0.005 0.001 HIS B 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 7428) covalent geometry : angle 0.52828 / 0.28 (10107) SS BOND : bond 0.00737 / 0.37 ( 2) SS BOND : angle 1.06803 / 0.46 ( 4) hydrogen bonds : bond 0.05224 / 3.55 ( 366) hydrogen bonds : angle 4.37854 / 3.16 ( 1065) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 47 time to evaluate : 0.279 Fit side-chains REVERT: B 236 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7369 (pt0) REVERT: B 250 THR cc_start: 0.8545 (m) cc_final: 0.8290 (p) REVERT: A 244 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.8053 (pt0) REVERT: A 343 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.7406 (mtp85) outliers start: 19 outliers final: 9 residues processed: 62 average time/residue: 0.6639 time to fit residues: 43.3753 Evaluate side-chains 58 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 55 ASN Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 236 GLU Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 244 GLN Chi-restraints excluded: chain A residue 343 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: [26, 72, 4, 54, 8, 7, 23, 2, 39, 5, 43] chunk 26 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 54 optimal weight: 0.3980 chunk 8 optimal weight: 0.9980 chunk 7 optimal weight: 0.2980 chunk 23 optimal weight: 1.9990 chunk 2 optimal weight: 0.0970 chunk 39 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 = 0.3516 r_free = 0.3516 target = 0.127600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.104423 restraints weight = 9411.566| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.62 r_work: 0.3116 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8940 moved from start: 0.0977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7430 Z= 0.095 Angle : 0.475 7.032 10111 Z= 0.254 Chirality : 0.043 0.145 1186 Planarity : 0.003 0.031 1293 Dihedral : 9.145 59.899 1123 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.08 % Favored : 97.81 % Rotamer: Outliers : 2.02 % Allowed : 18.71 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % 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: 1.25 (0.27), residues: 961 helix: 2.31 (0.27), residues: 368 sheet: 1.27 (0.36), residues: 225 loop : -1.07 (0.29), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 147 TYR 0.015 0.001 TYR A 16 PHE 0.010 0.001 PHE A 62 TRP 0.012 0.002 TRP A 429 HIS 0.003 0.001 HIS B 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00203 / 0.10 ( 7428) covalent geometry : angle 0.47507 / 0.25 (10107) SS BOND : bond 0.00532 / 0.27 ( 2) SS BOND : angle 0.63127 / 0.25 ( 4) hydrogen bonds : bond 0.03929 / 2.69 ( 366) hydrogen bonds : angle 4.18779 / 3.03 ( 1065) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 51 time to evaluate : 0.288 Fit side-chains REVERT: B 47 ILE cc_start: 0.8205 (OUTLIER) cc_final: 0.7873 (mm) REVERT: A 244 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.7998 (pt0) REVERT: A 274 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7765 (mm-30) REVERT: A 343 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.7458 (mtp85) outliers start: 15 outliers final: 8 residues processed: 62 average time/residue: 0.6097 time to fit residues: 40.0221 Evaluate side-chains 60 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 46 CYS Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 244 GLN Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 343 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: [4, 74, 50, 91, 71, 64, 9, 78, 23, 17, 62] chunk 4 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 17 optimal weight: 0.2980 chunk 62 optimal weight: 5.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- 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 = 0.3491 r_free = 0.3491 target = 0.125418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.102049 restraints weight = 9342.247| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.63 r_work: 0.3073 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8973 moved from start: 0.0959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7430 Z= 0.122 Angle : 0.514 7.382 10111 Z= 0.274 Chirality : 0.045 0.143 1186 Planarity : 0.003 0.033 1293 Dihedral : 9.220 59.959 1123 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.81 % Favored : 97.09 % Rotamer: Outliers : 2.02 % Allowed : 18.71 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % 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: 1.18 (0.27), residues: 961 helix: 2.26 (0.27), residues: 368 sheet: 1.23 (0.36), residues: 230 loop : -1.14 (0.29), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 288 TYR 0.018 0.002 TYR A 16 PHE 0.008 0.001 PHE A 62 TRP 0.010 0.002 TRP A 429 HIS 0.004 0.001 HIS B 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 7428) covalent geometry : angle 0.51363 / 0.27 (10107) SS BOND : bond 0.00682 / 0.34 ( 2) SS BOND : angle 1.18856 / 0.48 ( 4) hydrogen bonds : bond 0.04870 / 3.31 ( 366) hydrogen bonds : angle 4.28111 / 3.10 ( 1065) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 49 time to evaluate : 0.233 Fit side-chains REVERT: B 47 ILE cc_start: 0.8321 (OUTLIER) cc_final: 0.8007 (mm) REVERT: A 244 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.8018 (pt0) REVERT: A 274 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7768 (mm-30) REVERT: A 343 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.7463 (mtp85) outliers start: 15 outliers final: 9 residues processed: 59 average time/residue: 0.6111 time to fit residues: 38.1324 Evaluate side-chains 62 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 46 CYS Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 244 GLN Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 343 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: [71, 15, 30, 40, 23, 91, 93, 43, 53, 31, 19] chunk 71 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 30 optimal weight: 0.0870 chunk 40 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 91 optimal weight: 0.4980 chunk 93 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 31 optimal weight: 0.0980 chunk 19 optimal weight: 4.9990 overall best weight: 1.1362 ------------------------------------------------------------------------------- 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 = 0.3485 r_free = 0.3485 target = 0.125016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.101600 restraints weight = 9408.940| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.63 r_work: 0.3075 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8978 moved from start: 0.0982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7430 Z= 0.130 Angle : 0.527 7.772 10111 Z= 0.281 Chirality : 0.045 0.145 1186 Planarity : 0.003 0.033 1293 Dihedral : 9.261 59.796 1123 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.71 % Favored : 97.19 % Rotamer: Outliers : 1.62 % Allowed : 19.25 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % 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: 1.17 (0.27), residues: 961 helix: 2.25 (0.27), residues: 368 sheet: 1.23 (0.36), residues: 230 loop : -1.14 (0.29), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 21 TYR 0.019 0.002 TYR A 16 PHE 0.007 0.001 PHE A 62 TRP 0.010 0.002 TRP A 429 HIS 0.005 0.001 HIS B 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 7428) covalent geometry : angle 0.52658 / 0.28 (10107) SS BOND : bond 0.00713 / 0.36 ( 2) SS BOND : angle 1.21557 / 0.50 ( 4) hydrogen bonds : bond 0.05075 / 3.45 ( 366) hydrogen bonds : angle 4.32536 / 3.13 ( 1065) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1922 Ramachandran restraints generated. 961 Oldfield, 0 Emsley, 961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 0.294 Fit side-chains REVERT: B 47 ILE cc_start: 0.8353 (OUTLIER) cc_final: 0.8022 (mm) REVERT: A 244 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.8006 (pt0) REVERT: A 343 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.7453 (mtp85) outliers start: 12 outliers final: 9 residues processed: 57 average time/residue: 0.6631 time to fit residues: 39.9363 Evaluate side-chains 59 residues out of total 749 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 46 CYS Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 335 GLU Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 244 GLN Chi-restraints excluded: chain A residue 343 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: [32, 38, 0, 21, 3, 91, 33, 5, 86, 10, 31] chunk 32 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 33 optimal weight: 0.0770 chunk 5 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 31 optimal weight: 0.0270 overall best weight: 0.5600 ------------------------------------------------------------------------------- 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 = 0.3519 r_free = 0.3519 target = 0.127712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.104414 restraints weight = 9358.525| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.63 r_work: 0.3115 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7430 Z= 0.097 Angle : 0.478 7.553 10111 Z= 0.255 Chirality : 0.044 0.144 1186 Planarity : 0.003 0.031 1293 Dihedral : 8.936 59.691 1123 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.50 % Favored : 97.40 % Rotamer: Outliers : 1.62 % Allowed : 19.25 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % 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: 1.37 (0.27), residues: 961 helix: 2.42 (0.27), residues: 369 sheet: 1.32 (0.36), residues: 225 loop : -1.01 (0.29), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 147 TYR 0.015 0.001 TYR A 16 PHE 0.009 0.001 PHE A 62 TRP 0.012 0.002 TRP A 429 HIS 0.003 0.001 HIS B 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 ( 7428) covalent geometry : angle 0.47760 / 0.26 (10107) SS BOND : bond 0.00406 / 0.20 ( 2) SS BOND : angle 0.89510 / 0.36 ( 4) hydrogen bonds : bond 0.03931 / 2.68 ( 366) hydrogen bonds : angle 4.15121 / 3.01 ( 1065) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2523.68 seconds wall clock time: 43 minutes 42.43 seconds (2622.43 seconds total)