Starting phenix.real_space_refine on Sun May 3 10:10:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11mx_75851/05_2026/11mx_75851.cif Found real_map, /net/cci-nas-00/data/ceres_data/11mx_75851/05_2026/11mx_75851.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/11mx_75851/05_2026/11mx_75851.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11mx_75851/05_2026/11mx_75851.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/11mx_75851/05_2026/11mx_75851.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11mx_75851/05_2026/11mx_75851.map" } resolution = 2.94 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 51 5.16 5 C 7341 2.51 5 N 1998 2.21 5 O 2716 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12106 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 490, 3880 Classifications: {'peptide': 490} Link IDs: {'PTRANS': 20, 'TRANS': 469} Chain breaks: 1 Chain: "B" Number of atoms: 3880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 490, 3880 Classifications: {'peptide': 490} Link IDs: {'PTRANS': 20, 'TRANS': 469} Chain breaks: 1 Chain: "C" Number of atoms: 3880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 490, 3880 Classifications: {'peptide': 490} Link IDs: {'PTRANS': 20, 'TRANS': 469} Chain breaks: 1 Chain: "A" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 149 Classifications: {'water': 149} Link IDs: {None: 148} Chain: "B" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 148 Classifications: {'water': 148} Link IDs: {None: 147} Chain: "C" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 169 Classifications: {'water': 169} Link IDs: {None: 168} Time building chain proxies: 3.17, per 1000 atoms: 0.26 Number of scatterers: 12106 At special positions: 0 Unit cell: (85.26, 87.465, 149.205, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 51 16.00 O 2716 8.00 N 1998 7.00 C 7341 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 21 " - pdb=" SG CYS A 481 " distance=2.04 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 292 " distance=2.05 Simple disulfide: pdb=" SG CYS A 72 " - pdb=" SG CYS A 84 " distance=2.01 Simple disulfide: pdb=" SG CYS A 107 " - pdb=" SG CYS A 153 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 320 " distance=2.02 Simple disulfide: pdb=" SG CYS A 488 " - pdb=" SG CYS A 492 " distance=2.03 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 481 " distance=2.03 Simple disulfide: pdb=" SG CYS B 72 " - pdb=" SG CYS B 84 " distance=2.03 Simple disulfide: pdb=" SG CYS B 107 " - pdb=" SG CYS B 153 " distance=2.03 Simple disulfide: pdb=" SG CYS B 296 " - pdb=" SG CYS B 320 " distance=2.03 Simple disulfide: pdb=" SG CYS B 488 " - pdb=" SG CYS B 492 " distance=2.03 Simple disulfide: pdb=" SG CYS C 21 " - pdb=" SG CYS C 481 " distance=2.03 Simple disulfide: pdb=" SG CYS C 72 " - pdb=" SG CYS C 84 " distance=2.03 Simple disulfide: pdb=" SG CYS C 107 " - pdb=" SG CYS C 153 " distance=2.01 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 320 " distance=2.02 Simple disulfide: pdb=" SG CYS C 488 " - pdb=" SG CYS C 492 " 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: 0.73 Conformation dependent library (CDL) restraints added in 632.3 milliseconds 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2730 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 33 sheets defined 27.7% alpha, 25.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 73 through 80 Processing helix chain 'A' and resid 81 through 85 Processing helix chain 'A' and resid 114 through 122 Processing helix chain 'A' and resid 135 through 140 removed outlier: 4.480A pdb=" N TRP A 140 " --> pdb=" O LYS A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 209 Processing helix chain 'A' and resid 382 through 402 Processing helix chain 'A' and resid 418 through 470 removed outlier: 3.538A pdb=" N LEU A 470 " --> pdb=" O VAL A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 498 Processing helix chain 'A' and resid 502 through 516 removed outlier: 3.994A pdb=" N TYR A 506 " --> pdb=" O ASP A 502 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLU A 508 " --> pdb=" O PRO A 504 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N GLU A 509 " --> pdb=" O LYS A 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 80 Processing helix chain 'B' and resid 81 through 85 removed outlier: 3.631A pdb=" N GLU B 85 " --> pdb=" O PRO B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 122 Processing helix chain 'B' and resid 201 through 210 Processing helix chain 'B' and resid 382 through 402 Processing helix chain 'B' and resid 418 through 470 Processing helix chain 'B' and resid 489 through 498 Processing helix chain 'B' and resid 502 through 516 removed outlier: 3.662A pdb=" N TYR B 506 " --> pdb=" O ASP B 502 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLU B 508 " --> pdb=" O PRO B 504 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N GLU B 509 " --> pdb=" O LYS B 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 80 Processing helix chain 'C' and resid 81 through 87 removed outlier: 3.709A pdb=" N GLU C 85 " --> pdb=" O PRO C 82 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N SER C 86 " --> pdb=" O GLU C 83 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU C 87 " --> pdb=" O CYS C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 122 Processing helix chain 'C' and resid 135 through 140 removed outlier: 4.741A pdb=" N TRP C 140 " --> pdb=" O LYS C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 210 Processing helix chain 'C' and resid 381 through 403 removed outlier: 3.565A pdb=" N VAL C 399 " --> pdb=" O LYS C 395 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE C 400 " --> pdb=" O VAL C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 469 Processing helix chain 'C' and resid 489 through 499 Processing helix chain 'C' and resid 502 through 515 removed outlier: 4.196A pdb=" N TYR C 506 " --> pdb=" O ASP C 502 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N GLU C 509 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU C 512 " --> pdb=" O GLU C 508 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 376 through 380 removed outlier: 3.733A pdb=" N CYS A 21 " --> pdb=" O HIS A 369 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 33 Processing sheet with id=AA3, first strand: chain 'A' and resid 46 through 48 Processing sheet with id=AA4, first strand: chain 'A' and resid 50 through 51 Processing sheet with id=AA5, first strand: chain 'A' and resid 58 through 61 removed outlier: 5.548A pdb=" N LEU A 58 " --> pdb=" O HIS A 290 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N CYS A 292 " --> pdb=" O LEU A 58 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 67 through 69 removed outlier: 6.215A pdb=" N ILE A 96 " --> pdb=" O ILE A 283 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 125 through 132 removed outlier: 6.404A pdb=" N GLU A 275 " --> pdb=" O SER A 126 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N PHE A 128 " --> pdb=" O ALA A 273 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ALA A 273 " --> pdb=" O PHE A 128 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ARG A 130 " --> pdb=" O ALA A 271 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ALA A 271 " --> pdb=" O ARG A 130 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N TYR A 270 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N LEU A 193 " --> pdb=" O TYR A 270 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N LEU A 193 " --> pdb=" O PRO A 268 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 125 through 132 removed outlier: 6.404A pdb=" N GLU A 275 " --> pdb=" O SER A 126 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N PHE A 128 " --> pdb=" O ALA A 273 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ALA A 273 " --> pdb=" O PHE A 128 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ARG A 130 " --> pdb=" O ALA A 271 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ALA A 271 " --> pdb=" O ARG A 130 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N TYR A 270 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N LEU A 193 " --> pdb=" O TYR A 270 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 150 through 155 removed outlier: 4.944A pdb=" N CYS A 153 " --> pdb=" O SER A 160 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 178 through 183 Processing sheet with id=AB2, first strand: chain 'A' and resid 302 through 303 removed outlier: 4.038A pdb=" N CYS A 296 " --> pdb=" O ILE A 303 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 376 through 380 Processing sheet with id=AB4, first strand: chain 'B' and resid 32 through 33 Processing sheet with id=AB5, first strand: chain 'B' and resid 47 through 48 Processing sheet with id=AB6, first strand: chain 'B' and resid 50 through 51 Processing sheet with id=AB7, first strand: chain 'B' and resid 58 through 61 removed outlier: 5.624A pdb=" N LEU B 58 " --> pdb=" O HIS B 290 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N CYS B 292 " --> pdb=" O LEU B 58 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 67 through 69 removed outlier: 6.343A pdb=" N LEU B 67 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ILE B 96 " --> pdb=" O ILE B 283 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 125 through 131 removed outlier: 4.021A pdb=" N SER B 127 " --> pdb=" O GLU B 275 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N LEU B 193 " --> pdb=" O PRO B 268 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 125 through 131 removed outlier: 4.021A pdb=" N SER B 127 " --> pdb=" O GLU B 275 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 150 through 155 removed outlier: 7.521A pdb=" N ALA B 152 " --> pdb=" O ALA B 158 " (cutoff:3.500A) removed outlier: 10.234A pdb=" N ALA B 158 " --> pdb=" O ALA B 152 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 178 through 183 Processing sheet with id=AC4, first strand: chain 'B' and resid 301 through 303 removed outlier: 3.899A pdb=" N CYS B 296 " --> pdb=" O ILE B 303 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 376 through 380 Processing sheet with id=AC6, first strand: chain 'C' and resid 32 through 33 Processing sheet with id=AC7, first strand: chain 'C' and resid 47 through 48 Processing sheet with id=AC8, first strand: chain 'C' and resid 50 through 51 Processing sheet with id=AC9, first strand: chain 'C' and resid 58 through 61 removed outlier: 5.448A pdb=" N LEU C 58 " --> pdb=" O HIS C 290 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N CYS C 292 " --> pdb=" O LEU C 58 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 67 through 69 removed outlier: 6.344A pdb=" N ILE C 96 " --> pdb=" O ILE C 283 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 125 through 132 removed outlier: 3.622A pdb=" N SER C 127 " --> pdb=" O GLU C 275 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N TYR C 270 " --> pdb=" O LEU C 193 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N LEU C 193 " --> pdb=" O TYR C 270 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU C 189 " --> pdb=" O MET C 274 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N LEU C 193 " --> pdb=" O PRO C 268 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 125 through 132 removed outlier: 3.622A pdb=" N SER C 127 " --> pdb=" O GLU C 275 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N TYR C 270 " --> pdb=" O LEU C 193 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N LEU C 193 " --> pdb=" O TYR C 270 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU C 189 " --> pdb=" O MET C 274 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 150 through 155 removed outlier: 4.638A pdb=" N CYS C 153 " --> pdb=" O SER C 160 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 178 through 183 Processing sheet with id=AD6, first strand: chain 'C' and resid 302 through 303 removed outlier: 3.669A pdb=" N CYS C 296 " --> pdb=" O ILE C 303 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR C 408 " --> pdb=" O GLY C 318 " (cutoff:3.500A) 497 hydrogen bonds defined for protein. 1395 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: 1.90 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1990 1.32 - 1.45: 3271 1.45 - 1.58: 6586 1.58 - 1.70: 0 1.70 - 1.83: 66 Bond restraints: 11913 Sorted by residual: bond pdb=" N ILE B 282 " pdb=" CA ILE B 282 " ideal model delta sigma weight residual 1.459 1.505 -0.046 1.19e-02 7.06e+03 1.52e+01 bond pdb=" CA SER A 280 " pdb=" CB SER A 280 " ideal model delta sigma weight residual 1.532 1.464 0.068 1.79e-02 3.12e+03 1.45e+01 bond pdb=" N ARG A 276 " pdb=" CA ARG A 276 " ideal model delta sigma weight residual 1.454 1.503 -0.049 1.34e-02 5.57e+03 1.34e+01 bond pdb=" N ILE A 282 " pdb=" CA ILE A 282 " ideal model delta sigma weight residual 1.459 1.501 -0.042 1.19e-02 7.06e+03 1.24e+01 bond pdb=" C PRO C 154 " pdb=" O PRO C 154 " ideal model delta sigma weight residual 1.235 1.190 0.045 1.30e-02 5.92e+03 1.20e+01 ... (remaining 11908 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 14682 1.53 - 3.06: 1210 3.06 - 4.59: 206 4.59 - 6.12: 33 6.12 - 7.65: 9 Bond angle restraints: 16140 Sorted by residual: angle pdb=" CA GLN C 469 " pdb=" C GLN C 469 " pdb=" N LEU C 470 " ideal model delta sigma weight residual 115.30 122.61 -7.31 1.33e+00 5.65e-01 3.02e+01 angle pdb=" N ALA A 278 " pdb=" CA ALA A 278 " pdb=" C ALA A 278 " ideal model delta sigma weight residual 110.28 117.53 -7.25 1.48e+00 4.57e-01 2.40e+01 angle pdb=" O GLN C 469 " pdb=" C GLN C 469 " pdb=" N LEU C 470 " ideal model delta sigma weight residual 122.75 117.31 5.44 1.17e+00 7.31e-01 2.16e+01 angle pdb=" CA VAL C 466 " pdb=" C VAL C 466 " pdb=" N ARG C 467 " ideal model delta sigma weight residual 117.69 123.58 -5.89 1.27e+00 6.20e-01 2.15e+01 angle pdb=" N THR C 287 " pdb=" CA THR C 287 " pdb=" C THR C 287 " ideal model delta sigma weight residual 109.83 103.94 5.89 1.27e+00 6.20e-01 2.15e+01 ... (remaining 16135 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 6469 17.83 - 35.66: 509 35.66 - 53.49: 109 53.49 - 71.32: 42 71.32 - 89.15: 14 Dihedral angle restraints: 7143 sinusoidal: 2880 harmonic: 4263 Sorted by residual: dihedral pdb=" CB CYS A 72 " pdb=" SG CYS A 72 " pdb=" SG CYS A 84 " pdb=" CB CYS A 84 " ideal model delta sinusoidal sigma weight residual -86.00 -116.94 30.94 1 1.00e+01 1.00e-02 1.37e+01 dihedral pdb=" CA ALA C 278 " pdb=" C ALA C 278 " pdb=" N GLY C 279 " pdb=" CA GLY C 279 " ideal model delta harmonic sigma weight residual 180.00 162.60 17.40 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA ASP A 103 " pdb=" C ASP A 103 " pdb=" N ASN A 104 " pdb=" CA ASN A 104 " ideal model delta harmonic sigma weight residual -180.00 -162.63 -17.37 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 7140 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1268 0.056 - 0.112: 341 0.112 - 0.168: 106 0.168 - 0.224: 21 0.224 - 0.280: 7 Chirality restraints: 1743 Sorted by residual: chirality pdb=" CB VAL C 399 " pdb=" CA VAL C 399 " pdb=" CG1 VAL C 399 " pdb=" CG2 VAL C 399 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CA VAL B 216 " pdb=" N VAL B 216 " pdb=" C VAL B 216 " pdb=" CB VAL B 216 " both_signs ideal model delta sigma weight residual False 2.44 2.71 -0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA SER A 280 " pdb=" N SER A 280 " pdb=" C SER A 280 " pdb=" CB SER A 280 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 1740 not shown) Planarity restraints: 2088 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN C 469 " -0.024 2.00e-02 2.50e+03 4.65e-02 2.16e+01 pdb=" C GLN C 469 " 0.080 2.00e-02 2.50e+03 pdb=" O GLN C 469 " -0.028 2.00e-02 2.50e+03 pdb=" N LEU C 470 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 469 " 0.014 2.00e-02 2.50e+03 2.71e-02 7.36e+00 pdb=" C GLN B 469 " -0.047 2.00e-02 2.50e+03 pdb=" O GLN B 469 " 0.018 2.00e-02 2.50e+03 pdb=" N LEU B 470 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 233 " -0.013 2.00e-02 2.50e+03 2.71e-02 7.34e+00 pdb=" C ILE B 233 " 0.047 2.00e-02 2.50e+03 pdb=" O ILE B 233 " -0.018 2.00e-02 2.50e+03 pdb=" N ARG B 234 " -0.016 2.00e-02 2.50e+03 ... (remaining 2085 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 290 2.67 - 3.23: 10940 3.23 - 3.79: 19343 3.79 - 4.34: 27661 4.34 - 4.90: 45731 Nonbonded interactions: 103965 Sorted by model distance: nonbonded pdb=" O LEU B 470 " pdb=" CD1 LEU B 470 " model vdw 2.118 3.460 nonbonded pdb=" O SER B 94 " pdb=" OG SER B 280 " model vdw 2.251 3.040 nonbonded pdb=" O ASP A 291 " pdb=" OD1 ASP A 291 " model vdw 2.270 3.040 nonbonded pdb=" OD1 ASP A 213 " pdb=" O HOH A 601 " model vdw 2.304 3.040 nonbonded pdb=" OD2 ASP C 429 " pdb=" O HOH C 601 " model vdw 2.308 3.040 ... (remaining 103960 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 8.900 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.970 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 11929 Z= 0.438 Angle : 0.914 7.645 16172 Z= 0.624 Chirality : 0.061 0.280 1743 Planarity : 0.005 0.046 2088 Dihedral : 14.421 89.146 4365 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.09 % Allowed : 3.42 % Favored : 95.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.20), residues: 1458 helix: 1.28 (0.26), residues: 378 sheet: 0.17 (0.30), residues: 282 loop : -0.73 (0.20), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 467 TYR 0.025 0.002 TYR B 115 PHE 0.032 0.002 PHE A 112 TRP 0.019 0.002 TRP C 93 HIS 0.009 0.001 HIS B 370 Details of bonding type rmsd covalent geometry : bond 0.00668 (11913) covalent geometry : angle 0.91084 (16140) SS BOND : bond 0.00931 ( 16) SS BOND : angle 1.86432 ( 32) hydrogen bonds : bond 0.12935 ( 479) hydrogen bonds : angle 6.60751 ( 1395) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 242 time to evaluate : 0.464 Fit side-chains revert: symmetry clash REVERT: A 204 ASP cc_start: 0.7713 (t70) cc_final: 0.7435 (m-30) REVERT: A 290 HIS cc_start: 0.6501 (t-90) cc_final: 0.6179 (m90) REVERT: A 401 GLU cc_start: 0.8325 (mt-10) cc_final: 0.8064 (mm-30) REVERT: A 453 ASP cc_start: 0.7608 (m-30) cc_final: 0.7245 (t0) REVERT: A 460 LYS cc_start: 0.7416 (tptm) cc_final: 0.6851 (tmtt) REVERT: A 493 MET cc_start: 0.6966 (mmt) cc_final: 0.6737 (mmp) REVERT: B 38 GLU cc_start: 0.8221 (pm20) cc_final: 0.7680 (pm20) REVERT: B 71 LYS cc_start: 0.8209 (mtmt) cc_final: 0.7601 (mmpt) REVERT: B 163 LYS cc_start: 0.8536 (mttt) cc_final: 0.8300 (mmpt) REVERT: B 464 GLU cc_start: 0.7032 (mt-10) cc_final: 0.6830 (mm-30) REVERT: B 467 ARG cc_start: 0.7462 (ttp-170) cc_final: 0.6967 (ttm170) REVERT: C 71 LYS cc_start: 0.7712 (pttt) cc_final: 0.7262 (mttt) REVERT: C 222 ARG cc_start: 0.8940 (mtt-85) cc_final: 0.8586 (mtm180) REVERT: C 292 CYS cc_start: 0.7008 (t) cc_final: 0.6164 (m) REVERT: C 450 ARG cc_start: 0.8082 (mtp85) cc_final: 0.7537 (mmt-90) REVERT: C 467 ARG cc_start: 0.7123 (ptm-80) cc_final: 0.6774 (ptp-170) REVERT: C 502 ASP cc_start: 0.7277 (t70) cc_final: 0.6583 (p0) outliers start: 14 outliers final: 1 residues processed: 252 average time/residue: 0.6347 time to fit residues: 171.7943 Evaluate side-chains 113 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 112 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 153 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 0.0270 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 ASN B 45 HIS B 121 GLN B 173 ASN B 245 ASN B 290 HIS B 370 HIS C 25 HIS C 198 HIS C 205 GLN C 245 ASN C 369 HIS C 415 ASN C 423 ASN C 469 GLN C 490 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.144485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.118439 restraints weight = 14247.001| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.42 r_work: 0.3261 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 11929 Z= 0.118 Angle : 0.521 7.221 16172 Z= 0.279 Chirality : 0.042 0.181 1743 Planarity : 0.004 0.040 2088 Dihedral : 4.580 59.475 1579 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.25 % Allowed : 10.80 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.21), residues: 1458 helix: 2.16 (0.26), residues: 375 sheet: 0.04 (0.31), residues: 270 loop : -0.83 (0.19), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 450 TYR 0.017 0.001 TYR A 463 PHE 0.010 0.001 PHE C 112 TRP 0.009 0.001 TRP C 365 HIS 0.015 0.001 HIS B 370 Details of bonding type rmsd covalent geometry : bond 0.00267 (11913) covalent geometry : angle 0.51430 (16140) SS BOND : bond 0.00382 ( 16) SS BOND : angle 1.91442 ( 32) hydrogen bonds : bond 0.04486 ( 479) hydrogen bonds : angle 5.34065 ( 1395) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 144 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: A 275 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7777 (mt-10) REVERT: A 290 HIS cc_start: 0.6914 (t-90) cc_final: 0.6581 (m170) REVERT: A 319 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.7810 (mtmt) REVERT: A 453 ASP cc_start: 0.7597 (m-30) cc_final: 0.7389 (t0) REVERT: A 460 LYS cc_start: 0.7778 (tptm) cc_final: 0.7359 (tmtt) REVERT: B 71 LYS cc_start: 0.8012 (mtmt) cc_final: 0.7631 (mmpt) REVERT: B 467 ARG cc_start: 0.7525 (ttp-170) cc_final: 0.6847 (ttm170) REVERT: C 71 LYS cc_start: 0.7758 (pttt) cc_final: 0.7268 (mttt) REVERT: C 400 ILE cc_start: 0.7072 (OUTLIER) cc_final: 0.6025 (mm) REVERT: C 450 ARG cc_start: 0.7830 (mtp85) cc_final: 0.7467 (mmt-90) REVERT: C 460 LYS cc_start: 0.7674 (OUTLIER) cc_final: 0.7266 (tmtt) REVERT: C 502 ASP cc_start: 0.7018 (t70) cc_final: 0.6454 (p0) REVERT: C 505 LYS cc_start: 0.7037 (ptmt) cc_final: 0.6777 (pttt) outliers start: 29 outliers final: 7 residues processed: 167 average time/residue: 0.6341 time to fit residues: 114.0964 Evaluate side-chains 117 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 LYS Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 490 ASN Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 153 CYS Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 460 LYS Chi-restraints excluded: chain C residue 490 ASN Chi-restraints excluded: chain C residue 496 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 66 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 45 optimal weight: 0.5980 chunk 113 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 48 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN A 397 ASN A 472 ASN B 81 ASN B 173 ASN ** B 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 ASN B 370 HIS B 394 ASN B 415 ASN C 68 HIS C 490 ASN C 498 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.139080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.112913 restraints weight = 14569.810| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.56 r_work: 0.3164 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 11929 Z= 0.185 Angle : 0.565 7.199 16172 Z= 0.303 Chirality : 0.044 0.198 1743 Planarity : 0.004 0.042 2088 Dihedral : 4.701 52.401 1579 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.42 % Allowed : 11.58 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.21), residues: 1458 helix: 2.07 (0.26), residues: 375 sheet: -0.02 (0.30), residues: 288 loop : -0.73 (0.19), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 467 TYR 0.016 0.002 TYR A 463 PHE 0.013 0.002 PHE C 484 TRP 0.008 0.001 TRP C 93 HIS 0.016 0.002 HIS B 370 Details of bonding type rmsd covalent geometry : bond 0.00449 (11913) covalent geometry : angle 0.55820 (16140) SS BOND : bond 0.00632 ( 16) SS BOND : angle 1.97879 ( 32) hydrogen bonds : bond 0.04760 ( 479) hydrogen bonds : angle 5.29646 ( 1395) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 113 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: A 120 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7661 (tp30) REVERT: A 275 GLU cc_start: 0.8254 (mt-10) cc_final: 0.8015 (mt-10) REVERT: A 319 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.7806 (mtmt) REVERT: A 453 ASP cc_start: 0.7674 (m-30) cc_final: 0.7471 (t0) REVERT: A 460 LYS cc_start: 0.7799 (tptm) cc_final: 0.7375 (tmtt) REVERT: A 467 ARG cc_start: 0.8058 (ttp80) cc_final: 0.7748 (ttp80) REVERT: A 471 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.7944 (mptt) REVERT: A 493 MET cc_start: 0.7271 (mmt) cc_final: 0.6836 (mmp) REVERT: B 71 LYS cc_start: 0.8081 (mtmt) cc_final: 0.7563 (mmpt) REVERT: B 467 ARG cc_start: 0.7440 (ttp-170) cc_final: 0.7099 (ttm170) REVERT: C 71 LYS cc_start: 0.7895 (pttt) cc_final: 0.7414 (mtmt) REVERT: C 401 GLU cc_start: 0.7743 (pt0) cc_final: 0.7330 (mm-30) REVERT: C 450 ARG cc_start: 0.7908 (mtp85) cc_final: 0.7396 (mmt-90) REVERT: C 460 LYS cc_start: 0.7801 (OUTLIER) cc_final: 0.7320 (tmtt) REVERT: C 502 ASP cc_start: 0.7244 (t70) cc_final: 0.6698 (p0) outliers start: 44 outliers final: 15 residues processed: 148 average time/residue: 0.6480 time to fit residues: 103.1789 Evaluate side-chains 115 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 319 LYS Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 471 LYS Chi-restraints excluded: chain B residue 25 HIS Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 153 CYS Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 460 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 22 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 75 optimal weight: 0.6980 chunk 86 optimal weight: 2.9990 chunk 44 optimal weight: 8.9990 chunk 144 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 92 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 458 ASN B 240 GLN B 370 HIS C 490 ASN C 498 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.137141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.110936 restraints weight = 14571.564| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.51 r_work: 0.3159 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 11929 Z= 0.220 Angle : 0.595 12.080 16172 Z= 0.316 Chirality : 0.045 0.214 1743 Planarity : 0.004 0.040 2088 Dihedral : 4.793 47.678 1579 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.73 % Allowed : 12.98 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.20), residues: 1458 helix: 1.93 (0.26), residues: 375 sheet: -0.06 (0.31), residues: 270 loop : -0.86 (0.19), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 467 TYR 0.015 0.002 TYR A 454 PHE 0.016 0.002 PHE A 482 TRP 0.009 0.001 TRP B 358 HIS 0.015 0.002 HIS B 370 Details of bonding type rmsd covalent geometry : bond 0.00535 (11913) covalent geometry : angle 0.58796 (16140) SS BOND : bond 0.00674 ( 16) SS BOND : angle 2.10038 ( 32) hydrogen bonds : bond 0.04902 ( 479) hydrogen bonds : angle 5.25880 ( 1395) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 103 time to evaluate : 0.422 Fit side-chains REVERT: A 120 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7712 (tp30) REVERT: A 275 GLU cc_start: 0.8403 (mt-10) cc_final: 0.8107 (mt-10) REVERT: A 319 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.7757 (mtmt) REVERT: A 421 ILE cc_start: 0.8512 (OUTLIER) cc_final: 0.8286 (mm) REVERT: A 453 ASP cc_start: 0.7678 (m-30) cc_final: 0.7433 (t0) REVERT: A 460 LYS cc_start: 0.7811 (tptm) cc_final: 0.7243 (tttt) REVERT: B 71 LYS cc_start: 0.7999 (mtmt) cc_final: 0.7405 (mmpt) REVERT: B 120 GLU cc_start: 0.8398 (tp30) cc_final: 0.8092 (tp30) REVERT: B 467 ARG cc_start: 0.7339 (ttp-170) cc_final: 0.6899 (ttm170) REVERT: B 489 ASP cc_start: 0.5809 (t0) cc_final: 0.5305 (p0) REVERT: C 71 LYS cc_start: 0.7952 (pttt) cc_final: 0.7372 (mttt) REVERT: C 401 GLU cc_start: 0.7787 (pt0) cc_final: 0.7315 (mm-30) REVERT: C 460 LYS cc_start: 0.7778 (OUTLIER) cc_final: 0.7246 (tmtt) REVERT: C 502 ASP cc_start: 0.7287 (t70) cc_final: 0.6759 (p0) outliers start: 48 outliers final: 19 residues processed: 141 average time/residue: 0.6218 time to fit residues: 94.6389 Evaluate side-chains 119 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 319 LYS Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain B residue 25 HIS Chi-restraints excluded: chain B residue 241 GLU Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 490 ASN Chi-restraints excluded: chain C residue 25 HIS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 38 GLU Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 153 CYS Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 460 LYS Chi-restraints excluded: chain C residue 490 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 83 optimal weight: 8.9990 chunk 135 optimal weight: 0.5980 chunk 91 optimal weight: 4.9990 chunk 145 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 81 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 142 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN B 142 ASN C 490 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.139127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.113484 restraints weight = 14477.121| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.57 r_work: 0.3160 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 11929 Z= 0.149 Angle : 0.519 10.052 16172 Z= 0.279 Chirality : 0.043 0.175 1743 Planarity : 0.004 0.040 2088 Dihedral : 4.524 47.823 1579 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.80 % Allowed : 13.83 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.20), residues: 1458 helix: 2.14 (0.26), residues: 375 sheet: -0.08 (0.31), residues: 270 loop : -0.84 (0.19), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 450 TYR 0.015 0.001 TYR A 454 PHE 0.018 0.001 PHE A 482 TRP 0.008 0.001 TRP C 93 HIS 0.015 0.001 HIS B 370 Details of bonding type rmsd covalent geometry : bond 0.00356 (11913) covalent geometry : angle 0.51335 (16140) SS BOND : bond 0.00678 ( 16) SS BOND : angle 1.76377 ( 32) hydrogen bonds : bond 0.04423 ( 479) hydrogen bonds : angle 5.02370 ( 1395) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 114 time to evaluate : 0.432 Fit side-chains REVERT: A 120 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7635 (tp30) REVERT: A 275 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8239 (mt-10) REVERT: A 290 HIS cc_start: 0.6974 (t-90) cc_final: 0.6576 (t-90) REVERT: A 319 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.7812 (mtmt) REVERT: A 453 ASP cc_start: 0.7723 (m-30) cc_final: 0.7473 (t0) REVERT: A 460 LYS cc_start: 0.7746 (tptm) cc_final: 0.7196 (tttt) REVERT: A 467 ARG cc_start: 0.7736 (ttp80) cc_final: 0.7487 (ttp80) REVERT: B 71 LYS cc_start: 0.8035 (mtmt) cc_final: 0.7465 (mmpt) REVERT: B 120 GLU cc_start: 0.8404 (tp30) cc_final: 0.8135 (tp30) REVERT: B 467 ARG cc_start: 0.7422 (ttp-170) cc_final: 0.7013 (ttp-170) REVERT: B 472 ASN cc_start: 0.7166 (m110) cc_final: 0.6477 (p0) REVERT: B 489 ASP cc_start: 0.5795 (t0) cc_final: 0.5419 (p0) REVERT: C 71 LYS cc_start: 0.7988 (pttt) cc_final: 0.7454 (mtmt) REVERT: C 400 ILE cc_start: 0.7805 (OUTLIER) cc_final: 0.7048 (mm) REVERT: C 401 GLU cc_start: 0.7817 (pt0) cc_final: 0.7335 (mm-30) REVERT: C 460 LYS cc_start: 0.7674 (OUTLIER) cc_final: 0.7215 (tmtt) outliers start: 36 outliers final: 22 residues processed: 145 average time/residue: 0.5920 time to fit residues: 92.9679 Evaluate side-chains 127 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 101 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 319 LYS Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain B residue 25 HIS Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 490 ASN Chi-restraints excluded: chain C residue 25 HIS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 38 GLU Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 153 CYS Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 460 LYS Chi-restraints excluded: chain C residue 490 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 93 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 120 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 133 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 chunk 136 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 HIS B 370 HIS C 205 GLN C 490 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.138203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.112969 restraints weight = 14444.962| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.36 r_work: 0.3202 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 11929 Z= 0.169 Angle : 0.545 10.196 16172 Z= 0.290 Chirality : 0.043 0.195 1743 Planarity : 0.004 0.041 2088 Dihedral : 4.593 47.200 1579 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.26 % Allowed : 13.68 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.20), residues: 1458 helix: 2.15 (0.25), residues: 375 sheet: -0.09 (0.31), residues: 270 loop : -0.84 (0.19), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 450 TYR 0.014 0.001 TYR A 454 PHE 0.017 0.002 PHE A 482 TRP 0.008 0.001 TRP C 93 HIS 0.014 0.001 HIS B 370 Details of bonding type rmsd covalent geometry : bond 0.00408 (11913) covalent geometry : angle 0.53567 (16140) SS BOND : bond 0.00651 ( 16) SS BOND : angle 2.30300 ( 32) hydrogen bonds : bond 0.04518 ( 479) hydrogen bonds : angle 5.14837 ( 1395) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 112 time to evaluate : 0.416 Fit side-chains REVERT: A 120 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7542 (tp30) REVERT: A 275 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8185 (mt-10) REVERT: A 290 HIS cc_start: 0.6881 (t-90) cc_final: 0.6279 (m90) REVERT: A 319 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.7792 (mtmt) REVERT: A 421 ILE cc_start: 0.8482 (OUTLIER) cc_final: 0.8254 (mm) REVERT: A 453 ASP cc_start: 0.7613 (m-30) cc_final: 0.7392 (t0) REVERT: A 460 LYS cc_start: 0.7691 (tptm) cc_final: 0.7121 (tttt) REVERT: A 467 ARG cc_start: 0.7679 (ttp80) cc_final: 0.7095 (ttp80) REVERT: A 468 SER cc_start: 0.8186 (OUTLIER) cc_final: 0.7911 (p) REVERT: A 493 MET cc_start: 0.7453 (mmt) cc_final: 0.6992 (mmp) REVERT: B 71 LYS cc_start: 0.8007 (mtmt) cc_final: 0.7471 (mmpt) REVERT: B 120 GLU cc_start: 0.8285 (tp30) cc_final: 0.8045 (tp30) REVERT: B 472 ASN cc_start: 0.7524 (m110) cc_final: 0.6705 (p0) REVERT: B 489 ASP cc_start: 0.5793 (t0) cc_final: 0.5531 (p0) REVERT: C 71 LYS cc_start: 0.8002 (pttt) cc_final: 0.7459 (mttt) REVERT: C 400 ILE cc_start: 0.7792 (OUTLIER) cc_final: 0.7121 (mm) REVERT: C 401 GLU cc_start: 0.7749 (pt0) cc_final: 0.7319 (mm-30) REVERT: C 450 ARG cc_start: 0.7597 (mtp85) cc_final: 0.6814 (mmt-90) REVERT: C 460 LYS cc_start: 0.7660 (OUTLIER) cc_final: 0.7173 (tmtt) REVERT: C 509 GLU cc_start: 0.6471 (tp30) cc_final: 0.6145 (tp30) REVERT: C 513 ASN cc_start: 0.6907 (OUTLIER) cc_final: 0.6606 (m110) outliers start: 42 outliers final: 28 residues processed: 145 average time/residue: 0.5700 time to fit residues: 90.0319 Evaluate side-chains 136 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 101 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 57 LYS Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 319 LYS Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain B residue 25 HIS Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 460 LYS Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain C residue 25 HIS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 38 GLU Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 153 CYS Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 460 LYS Chi-restraints excluded: chain C residue 490 ASN Chi-restraints excluded: chain C residue 513 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 13 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 96 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 130 optimal weight: 0.4980 chunk 19 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN C 490 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.139082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.113841 restraints weight = 14400.311| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.37 r_work: 0.3218 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 11929 Z= 0.145 Angle : 0.529 9.095 16172 Z= 0.282 Chirality : 0.043 0.212 1743 Planarity : 0.004 0.041 2088 Dihedral : 4.533 47.634 1579 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.57 % Allowed : 13.60 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.20), residues: 1458 helix: 2.22 (0.26), residues: 375 sheet: -0.08 (0.31), residues: 270 loop : -0.82 (0.19), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 450 TYR 0.012 0.001 TYR A 454 PHE 0.018 0.001 PHE A 482 TRP 0.008 0.001 TRP C 93 HIS 0.016 0.001 HIS B 370 Details of bonding type rmsd covalent geometry : bond 0.00344 (11913) covalent geometry : angle 0.51805 (16140) SS BOND : bond 0.00618 ( 16) SS BOND : angle 2.44163 ( 32) hydrogen bonds : bond 0.04357 ( 479) hydrogen bonds : angle 5.03448 ( 1395) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 110 time to evaluate : 0.465 Fit side-chains REVERT: A 120 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7549 (tp30) REVERT: A 275 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8172 (mt-10) REVERT: A 290 HIS cc_start: 0.6854 (t-90) cc_final: 0.6289 (m90) REVERT: A 319 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.7795 (mtmt) REVERT: A 421 ILE cc_start: 0.8472 (OUTLIER) cc_final: 0.8242 (mm) REVERT: A 453 ASP cc_start: 0.7589 (m-30) cc_final: 0.7373 (t0) REVERT: A 460 LYS cc_start: 0.7638 (tptm) cc_final: 0.7051 (tttt) REVERT: A 467 ARG cc_start: 0.7640 (ttp80) cc_final: 0.7075 (ttp80) REVERT: A 468 SER cc_start: 0.8181 (OUTLIER) cc_final: 0.7902 (p) REVERT: A 493 MET cc_start: 0.7475 (mmt) cc_final: 0.7021 (mmp) REVERT: B 71 LYS cc_start: 0.8008 (mtmt) cc_final: 0.7470 (mmpt) REVERT: B 120 GLU cc_start: 0.8271 (tp30) cc_final: 0.8038 (tp30) REVERT: B 401 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7403 (mt-10) REVERT: B 472 ASN cc_start: 0.7610 (m110) cc_final: 0.6777 (p0) REVERT: B 489 ASP cc_start: 0.5744 (t0) cc_final: 0.5536 (p0) REVERT: C 71 LYS cc_start: 0.7976 (pttt) cc_final: 0.7429 (mttt) REVERT: C 400 ILE cc_start: 0.7722 (OUTLIER) cc_final: 0.7003 (mm) REVERT: C 401 GLU cc_start: 0.7748 (pt0) cc_final: 0.7302 (mm-30) REVERT: C 450 ARG cc_start: 0.7587 (mtp85) cc_final: 0.6794 (mmt-90) REVERT: C 469 GLN cc_start: 0.6917 (OUTLIER) cc_final: 0.6591 (mt0) REVERT: C 492 CYS cc_start: 0.5304 (t) cc_final: 0.5087 (t) REVERT: C 509 GLU cc_start: 0.6486 (tp30) cc_final: 0.5971 (tp30) REVERT: C 513 ASN cc_start: 0.6869 (OUTLIER) cc_final: 0.6536 (m110) outliers start: 46 outliers final: 29 residues processed: 147 average time/residue: 0.6027 time to fit residues: 95.9923 Evaluate side-chains 140 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 103 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain A residue 319 LYS Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain B residue 25 HIS Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain C residue 25 HIS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 38 GLU Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 153 CYS Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 469 GLN Chi-restraints excluded: chain C residue 490 ASN Chi-restraints excluded: chain C residue 513 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 7 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 118 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 115 optimal weight: 0.4980 chunk 109 optimal weight: 0.8980 chunk 86 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 490 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.140729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.115494 restraints weight = 14246.893| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.37 r_work: 0.3239 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11929 Z= 0.119 Angle : 0.497 7.657 16172 Z= 0.266 Chirality : 0.042 0.155 1743 Planarity : 0.004 0.041 2088 Dihedral : 4.437 48.346 1579 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.64 % Allowed : 15.00 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.21), residues: 1458 helix: 2.39 (0.26), residues: 375 sheet: -0.03 (0.31), residues: 270 loop : -0.79 (0.19), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 276 TYR 0.020 0.001 TYR A 463 PHE 0.018 0.001 PHE A 482 TRP 0.008 0.001 TRP C 93 HIS 0.015 0.001 HIS B 370 Details of bonding type rmsd covalent geometry : bond 0.00275 (11913) covalent geometry : angle 0.48853 (16140) SS BOND : bond 0.00560 ( 16) SS BOND : angle 2.08520 ( 32) hydrogen bonds : bond 0.04126 ( 479) hydrogen bonds : angle 4.96019 ( 1395) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 113 time to evaluate : 0.522 Fit side-chains REVERT: A 120 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7519 (tp30) REVERT: A 275 GLU cc_start: 0.8374 (mt-10) cc_final: 0.8111 (mt-10) REVERT: A 290 HIS cc_start: 0.6832 (t-90) cc_final: 0.6337 (m90) REVERT: A 319 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.7787 (mtmt) REVERT: A 421 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.8211 (mm) REVERT: A 453 ASP cc_start: 0.7541 (m-30) cc_final: 0.7321 (t0) REVERT: A 460 LYS cc_start: 0.7573 (tptm) cc_final: 0.7091 (tmtt) REVERT: A 467 ARG cc_start: 0.7624 (ttp80) cc_final: 0.7379 (ttp80) REVERT: A 468 SER cc_start: 0.8151 (OUTLIER) cc_final: 0.7877 (p) REVERT: A 493 MET cc_start: 0.7466 (mmt) cc_final: 0.7015 (mmp) REVERT: B 71 LYS cc_start: 0.8016 (mtmt) cc_final: 0.7487 (mmpt) REVERT: B 120 GLU cc_start: 0.8242 (tp30) cc_final: 0.8021 (tp30) REVERT: B 401 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7314 (mp0) REVERT: B 472 ASN cc_start: 0.7575 (m110) cc_final: 0.6795 (p0) REVERT: C 71 LYS cc_start: 0.7970 (pttt) cc_final: 0.7425 (mtmt) REVERT: C 401 GLU cc_start: 0.7740 (pt0) cc_final: 0.7248 (mm-30) REVERT: C 450 ARG cc_start: 0.7567 (mtp85) cc_final: 0.6767 (mmt-90) REVERT: C 492 CYS cc_start: 0.5451 (t) cc_final: 0.5165 (t) REVERT: C 509 GLU cc_start: 0.6492 (tp30) cc_final: 0.5953 (tp30) REVERT: C 513 ASN cc_start: 0.6831 (OUTLIER) cc_final: 0.6485 (m110) outliers start: 34 outliers final: 18 residues processed: 140 average time/residue: 0.6049 time to fit residues: 91.7889 Evaluate side-chains 125 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 319 LYS Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 401 GLU Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain C residue 25 HIS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 153 CYS Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain C residue 513 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 90 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 135 optimal weight: 5.9990 chunk 13 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 141 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 370 HIS C 490 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.140771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.115136 restraints weight = 14281.621| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.42 r_work: 0.3226 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 11929 Z= 0.123 Angle : 0.507 8.762 16172 Z= 0.271 Chirality : 0.042 0.152 1743 Planarity : 0.004 0.041 2088 Dihedral : 4.451 48.443 1579 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.80 % Allowed : 15.31 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 (0.21), residues: 1458 helix: 2.39 (0.26), residues: 375 sheet: -0.02 (0.31), residues: 270 loop : -0.78 (0.19), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 276 TYR 0.022 0.001 TYR A 463 PHE 0.017 0.001 PHE A 482 TRP 0.008 0.001 TRP C 93 HIS 0.015 0.001 HIS B 370 Details of bonding type rmsd covalent geometry : bond 0.00287 (11913) covalent geometry : angle 0.49853 (16140) SS BOND : bond 0.00543 ( 16) SS BOND : angle 2.13237 ( 32) hydrogen bonds : bond 0.04129 ( 479) hydrogen bonds : angle 4.97370 ( 1395) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 108 time to evaluate : 0.494 Fit side-chains REVERT: A 120 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7587 (tp30) REVERT: A 275 GLU cc_start: 0.8349 (mt-10) cc_final: 0.8107 (mt-10) REVERT: A 290 HIS cc_start: 0.6787 (t-90) cc_final: 0.6379 (m90) REVERT: A 319 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.7841 (mtmt) REVERT: A 421 ILE cc_start: 0.8336 (OUTLIER) cc_final: 0.8053 (mm) REVERT: A 460 LYS cc_start: 0.7597 (tptm) cc_final: 0.7124 (tmtt) REVERT: A 468 SER cc_start: 0.8165 (OUTLIER) cc_final: 0.7896 (p) REVERT: B 71 LYS cc_start: 0.8023 (mtmt) cc_final: 0.7527 (mmpt) REVERT: B 120 GLU cc_start: 0.8277 (tp30) cc_final: 0.8065 (tp30) REVERT: B 472 ASN cc_start: 0.7630 (m110) cc_final: 0.6865 (p0) REVERT: C 71 LYS cc_start: 0.7969 (pttt) cc_final: 0.7443 (mtmt) REVERT: C 400 ILE cc_start: 0.7620 (OUTLIER) cc_final: 0.6558 (mm) REVERT: C 401 GLU cc_start: 0.7761 (pt0) cc_final: 0.7321 (mm-30) REVERT: C 450 ARG cc_start: 0.7645 (mtp85) cc_final: 0.6869 (mmt-90) REVERT: C 509 GLU cc_start: 0.6530 (tp30) cc_final: 0.5783 (tp30) REVERT: C 513 ASN cc_start: 0.6818 (OUTLIER) cc_final: 0.6352 (m110) outliers start: 36 outliers final: 23 residues processed: 137 average time/residue: 0.6061 time to fit residues: 90.0666 Evaluate side-chains 131 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 102 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 319 LYS Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain C residue 25 HIS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 153 CYS Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 490 ASN Chi-restraints excluded: chain C residue 513 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 63 optimal weight: 1.9990 chunk 50 optimal weight: 9.9990 chunk 129 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 35 optimal weight: 8.9990 chunk 67 optimal weight: 0.6980 chunk 118 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 ASN A 387 ASN B 370 HIS C 490 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.136690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.110631 restraints weight = 14471.053| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.49 r_work: 0.3149 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 11929 Z= 0.226 Angle : 0.606 9.274 16172 Z= 0.322 Chirality : 0.045 0.179 1743 Planarity : 0.004 0.042 2088 Dihedral : 4.847 46.607 1579 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.49 % Allowed : 16.01 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.04 (0.20), residues: 1458 helix: 1.97 (0.25), residues: 375 sheet: -0.11 (0.31), residues: 270 loop : -0.87 (0.19), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 467 TYR 0.025 0.002 TYR A 463 PHE 0.018 0.002 PHE C 482 TRP 0.010 0.001 TRP B 358 HIS 0.012 0.002 HIS B 370 Details of bonding type rmsd covalent geometry : bond 0.00551 (11913) covalent geometry : angle 0.59556 (16140) SS BOND : bond 0.00746 ( 16) SS BOND : angle 2.60523 ( 32) hydrogen bonds : bond 0.04807 ( 479) hydrogen bonds : angle 5.26397 ( 1395) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 104 time to evaluate : 0.509 Fit side-chains revert: symmetry clash REVERT: A 120 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7785 (tp30) REVERT: A 275 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8128 (mt-10) REVERT: A 290 HIS cc_start: 0.6725 (t-90) cc_final: 0.6238 (m90) REVERT: A 319 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.7774 (mtmt) REVERT: A 421 ILE cc_start: 0.8370 (OUTLIER) cc_final: 0.8058 (mm) REVERT: A 460 LYS cc_start: 0.7773 (tptm) cc_final: 0.7294 (tmtt) REVERT: A 493 MET cc_start: 0.7354 (mmt) cc_final: 0.6860 (mmp) REVERT: B 38 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7829 (pm20) REVERT: B 71 LYS cc_start: 0.8026 (mtmt) cc_final: 0.7427 (mmpt) REVERT: B 120 GLU cc_start: 0.8376 (tp30) cc_final: 0.8137 (tp30) REVERT: B 472 ASN cc_start: 0.7788 (m110) cc_final: 0.6990 (p0) REVERT: C 18 ASP cc_start: 0.6328 (m-30) cc_final: 0.6043 (m-30) REVERT: C 71 LYS cc_start: 0.8033 (pttt) cc_final: 0.7457 (mtmt) REVERT: C 401 GLU cc_start: 0.7816 (pt0) cc_final: 0.7308 (mm-30) REVERT: C 450 ARG cc_start: 0.7563 (mtp85) cc_final: 0.6760 (mmt-90) REVERT: C 509 GLU cc_start: 0.6503 (tp30) cc_final: 0.6046 (tp30) REVERT: C 513 ASN cc_start: 0.6988 (OUTLIER) cc_final: 0.6639 (m110) outliers start: 32 outliers final: 19 residues processed: 132 average time/residue: 0.6101 time to fit residues: 87.4127 Evaluate side-chains 125 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 319 LYS Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain C residue 25 HIS Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 153 CYS Chi-restraints excluded: chain C residue 202 SER Chi-restraints excluded: chain C residue 327 THR Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain C residue 490 ASN Chi-restraints excluded: chain C residue 513 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 100 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 127 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 111 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 45 optimal weight: 0.0970 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 490 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.140488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.115371 restraints weight = 14294.831| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.37 r_work: 0.3220 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11929 Z= 0.121 Angle : 0.510 7.686 16172 Z= 0.274 Chirality : 0.042 0.154 1743 Planarity : 0.004 0.041 2088 Dihedral : 4.547 48.674 1579 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.86 % Allowed : 16.55 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.19 (0.21), residues: 1458 helix: 2.21 (0.26), residues: 375 sheet: -0.05 (0.31), residues: 270 loop : -0.83 (0.19), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 276 TYR 0.020 0.001 TYR A 463 PHE 0.018 0.001 PHE A 482 TRP 0.007 0.001 TRP C 93 HIS 0.017 0.001 HIS B 370 Details of bonding type rmsd covalent geometry : bond 0.00281 (11913) covalent geometry : angle 0.50122 (16140) SS BOND : bond 0.00585 ( 16) SS BOND : angle 2.21671 ( 32) hydrogen bonds : bond 0.04153 ( 479) hydrogen bonds : angle 5.00586 ( 1395) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3790.51 seconds wall clock time: 65 minutes 45.92 seconds (3945.92 seconds total)