Starting phenix.real_space_refine on Wed Aug 5 21:32:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/21ff_67623/08_2026/21ff_67623.cif Found real_map, /net/cci-nas-00/data/ceres_data/21ff_67623/08_2026/21ff_67623.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/21ff_67623/08_2026/21ff_67623.map" default_real_map = "/net/cci-nas-00/data/ceres_data/21ff_67623/08_2026/21ff_67623.map" model { file = "/net/cci-nas-00/data/ceres_data/21ff_67623/08_2026/21ff_67623.cif" } default_model = "/net/cci-nas-00/data/ceres_data/21ff_67623/08_2026/21ff_67623.cif" } resolution = 2.8 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= 0.006 sd= 0.073 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 63 5.16 5 C 7782 2.51 5 N 1755 2.21 5 O 1989 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11589 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3863 Classifications: {'peptide': 500} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 20, 'TRANS': 479} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: B, C Time building chain proxies: 2.16, per 1000 atoms: 0.19 Number of scatterers: 11589 At special positions: 0 Unit cell: (114.48, 108.12, 75.26, 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 63 16.00 O 1989 8.00 N 1755 7.00 C 7782 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.71 Conformation dependent library (CDL) restraints added in 433.9 milliseconds 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2706 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 0 sheets defined 84.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 7 through 28 Proline residue: A 24 - end of helix Processing helix chain 'A' and resid 28 through 67 removed outlier: 5.745A pdb=" N MET A 49 " --> pdb=" O SER A 45 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N VAL A 50 " --> pdb=" O ASN A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 73 removed outlier: 3.563A pdb=" N LYS A 72 " --> pdb=" O GLU A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 96 Processing helix chain 'A' and resid 101 through 116 removed outlier: 4.064A pdb=" N THR A 107 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N TRP A 110 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N ALA A 111 " --> pdb=" O THR A 107 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TYR A 112 " --> pdb=" O ILE A 108 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR A 115 " --> pdb=" O ALA A 111 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA A 116 " --> pdb=" O TYR A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 139 Processing helix chain 'A' and resid 141 through 161 removed outlier: 4.066A pdb=" N PHE A 147 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N PHE A 148 " --> pdb=" O ALA A 144 " (cutoff:3.500A) Proline residue: A 151 - end of helix Proline residue: A 154 - end of helix Processing helix chain 'A' and resid 168 through 173 Processing helix chain 'A' and resid 173 through 178 Processing helix chain 'A' and resid 179 through 183 Processing helix chain 'A' and resid 188 through 220 removed outlier: 4.414A pdb=" N ILE A 197 " --> pdb=" O PHE A 193 " (cutoff:3.500A) Proline residue: A 210 - end of helix Processing helix chain 'A' and resid 227 through 247 Processing helix chain 'A' and resid 251 through 274 Processing helix chain 'A' and resid 275 through 293 Processing helix chain 'A' and resid 293 through 299 Processing helix chain 'A' and resid 308 through 313 Processing helix chain 'A' and resid 313 through 335 Proline residue: A 326 - end of helix Processing helix chain 'A' and resid 340 through 373 Processing helix chain 'A' and resid 377 through 383 removed outlier: 3.708A pdb=" N GLU A 383 " --> pdb=" O THR A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 397 Processing helix chain 'A' and resid 400 through 431 Processing helix chain 'A' and resid 442 through 454 removed outlier: 3.632A pdb=" N ARG A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 463 removed outlier: 3.608A pdb=" N VAL A 462 " --> pdb=" O GLY A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 479 removed outlier: 3.592A pdb=" N LEU A 470 " --> pdb=" O ASP A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 499 removed outlier: 3.937A pdb=" N VAL A 484 " --> pdb=" O PRO A 480 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY A 499 " --> pdb=" O MET A 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 28 Proline residue: B 24 - end of helix Processing helix chain 'B' and resid 28 through 67 removed outlier: 5.745A pdb=" N MET B 49 " --> pdb=" O SER B 45 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N VAL B 50 " --> pdb=" O ASN B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 73 removed outlier: 3.563A pdb=" N LYS B 72 " --> pdb=" O GLU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 96 Processing helix chain 'B' and resid 101 through 116 removed outlier: 4.063A pdb=" N THR B 107 " --> pdb=" O VAL B 103 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N TRP B 110 " --> pdb=" O GLY B 106 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N ALA B 111 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TYR B 112 " --> pdb=" O ILE B 108 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR B 115 " --> pdb=" O ALA B 111 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA B 116 " --> pdb=" O TYR B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 139 Processing helix chain 'B' and resid 141 through 161 removed outlier: 4.066A pdb=" N PHE B 147 " --> pdb=" O SER B 143 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N PHE B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) Proline residue: B 151 - end of helix Proline residue: B 154 - end of helix Processing helix chain 'B' and resid 168 through 173 Processing helix chain 'B' and resid 173 through 178 Processing helix chain 'B' and resid 179 through 183 Processing helix chain 'B' and resid 188 through 220 removed outlier: 4.414A pdb=" N ILE B 197 " --> pdb=" O PHE B 193 " (cutoff:3.500A) Proline residue: B 210 - end of helix Processing helix chain 'B' and resid 227 through 247 Processing helix chain 'B' and resid 251 through 274 Processing helix chain 'B' and resid 275 through 293 Processing helix chain 'B' and resid 293 through 299 Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'B' and resid 313 through 335 Proline residue: B 326 - end of helix Processing helix chain 'B' and resid 340 through 373 Processing helix chain 'B' and resid 377 through 383 removed outlier: 3.708A pdb=" N GLU B 383 " --> pdb=" O THR B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 397 Processing helix chain 'B' and resid 400 through 431 Processing helix chain 'B' and resid 442 through 454 removed outlier: 3.632A pdb=" N ARG B 446 " --> pdb=" O ALA B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 463 removed outlier: 3.608A pdb=" N VAL B 462 " --> pdb=" O GLY B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 479 removed outlier: 3.592A pdb=" N LEU B 470 " --> pdb=" O ASP B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 499 removed outlier: 3.937A pdb=" N VAL B 484 " --> pdb=" O PRO B 480 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY B 499 " --> pdb=" O MET B 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 28 Proline residue: C 24 - end of helix Processing helix chain 'C' and resid 28 through 67 removed outlier: 5.745A pdb=" N MET C 49 " --> pdb=" O SER C 45 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N VAL C 50 " --> pdb=" O ASN C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 73 removed outlier: 3.563A pdb=" N LYS C 72 " --> pdb=" O GLU C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 96 Processing helix chain 'C' and resid 101 through 116 removed outlier: 4.064A pdb=" N THR C 107 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N TRP C 110 " --> pdb=" O GLY C 106 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N ALA C 111 " --> pdb=" O THR C 107 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR C 112 " --> pdb=" O ILE C 108 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR C 115 " --> pdb=" O ALA C 111 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA C 116 " --> pdb=" O TYR C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 139 Processing helix chain 'C' and resid 141 through 161 removed outlier: 4.066A pdb=" N PHE C 147 " --> pdb=" O SER C 143 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N PHE C 148 " --> pdb=" O ALA C 144 " (cutoff:3.500A) Proline residue: C 151 - end of helix Proline residue: C 154 - end of helix Processing helix chain 'C' and resid 168 through 173 Processing helix chain 'C' and resid 173 through 178 Processing helix chain 'C' and resid 179 through 183 Processing helix chain 'C' and resid 188 through 220 removed outlier: 4.413A pdb=" N ILE C 197 " --> pdb=" O PHE C 193 " (cutoff:3.500A) Proline residue: C 210 - end of helix Processing helix chain 'C' and resid 227 through 247 Processing helix chain 'C' and resid 251 through 274 Processing helix chain 'C' and resid 275 through 293 Processing helix chain 'C' and resid 293 through 299 Processing helix chain 'C' and resid 308 through 313 Processing helix chain 'C' and resid 313 through 335 Proline residue: C 326 - end of helix Processing helix chain 'C' and resid 340 through 373 Processing helix chain 'C' and resid 377 through 383 removed outlier: 3.708A pdb=" N GLU C 383 " --> pdb=" O THR C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 397 Processing helix chain 'C' and resid 400 through 431 Processing helix chain 'C' and resid 442 through 454 removed outlier: 3.632A pdb=" N ARG C 446 " --> pdb=" O ALA C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 463 removed outlier: 3.608A pdb=" N VAL C 462 " --> pdb=" O GLY C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 479 removed outlier: 3.592A pdb=" N LEU C 470 " --> pdb=" O ASP C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 499 removed outlier: 3.937A pdb=" N VAL C 484 " --> pdb=" O PRO C 480 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY C 499 " --> pdb=" O MET C 495 " (cutoff:3.500A) 879 hydrogen bonds defined for protein. 2601 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: 1.54 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1725 1.31 - 1.43: 3459 1.43 - 1.56: 6636 1.56 - 1.68: 0 1.68 - 1.81: 108 Bond restraints: 11928 Sorted by residual: bond pdb=" CA TRP A 321 " pdb=" C TRP A 321 " ideal model delta sigma weight residual 1.523 1.463 0.060 1.35e-02 5.49e+03 1.97e+01 bond pdb=" CA LEU B 467 " pdb=" C LEU B 467 " ideal model delta sigma weight residual 1.523 1.462 0.061 1.37e-02 5.33e+03 1.97e+01 bond pdb=" CA TRP B 321 " pdb=" C TRP B 321 " ideal model delta sigma weight residual 1.523 1.463 0.060 1.35e-02 5.49e+03 1.97e+01 bond pdb=" CA TRP C 321 " pdb=" C TRP C 321 " ideal model delta sigma weight residual 1.523 1.463 0.060 1.35e-02 5.49e+03 1.96e+01 bond pdb=" CA LEU C 467 " pdb=" C LEU C 467 " ideal model delta sigma weight residual 1.523 1.462 0.061 1.37e-02 5.33e+03 1.95e+01 ... (remaining 11923 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 16004 2.27 - 4.53: 220 4.53 - 6.80: 27 6.80 - 9.07: 12 9.07 - 11.34: 3 Bond angle restraints: 16266 Sorted by residual: angle pdb=" N MET A 194 " pdb=" CA MET A 194 " pdb=" C MET A 194 " ideal model delta sigma weight residual 113.43 102.09 11.34 1.26e+00 6.30e-01 8.09e+01 angle pdb=" N MET C 194 " pdb=" CA MET C 194 " pdb=" C MET C 194 " ideal model delta sigma weight residual 113.43 102.10 11.33 1.26e+00 6.30e-01 8.09e+01 angle pdb=" N MET B 194 " pdb=" CA MET B 194 " pdb=" C MET B 194 " ideal model delta sigma weight residual 113.43 102.12 11.31 1.26e+00 6.30e-01 8.06e+01 angle pdb=" N TYR C 324 " pdb=" CA TYR C 324 " pdb=" C TYR C 324 " ideal model delta sigma weight residual 113.18 104.44 8.74 1.21e+00 6.83e-01 5.22e+01 angle pdb=" N TYR B 324 " pdb=" CA TYR B 324 " pdb=" C TYR B 324 " ideal model delta sigma weight residual 113.18 104.47 8.71 1.21e+00 6.83e-01 5.19e+01 ... (remaining 16261 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.43: 5996 15.43 - 30.85: 580 30.85 - 46.27: 120 46.27 - 61.70: 27 61.70 - 77.12: 6 Dihedral angle restraints: 6729 sinusoidal: 2472 harmonic: 4257 Sorted by residual: dihedral pdb=" N PHE B 193 " pdb=" C PHE B 193 " pdb=" CA PHE B 193 " pdb=" CB PHE B 193 " ideal model delta harmonic sigma weight residual 122.80 113.24 9.56 0 2.50e+00 1.60e-01 1.46e+01 dihedral pdb=" N PHE A 193 " pdb=" C PHE A 193 " pdb=" CA PHE A 193 " pdb=" CB PHE A 193 " ideal model delta harmonic sigma weight residual 122.80 113.25 9.55 0 2.50e+00 1.60e-01 1.46e+01 dihedral pdb=" N PHE C 193 " pdb=" C PHE C 193 " pdb=" CA PHE C 193 " pdb=" CB PHE C 193 " ideal model delta harmonic sigma weight residual 122.80 113.27 9.53 0 2.50e+00 1.60e-01 1.45e+01 ... (remaining 6726 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1309 0.035 - 0.069: 414 0.069 - 0.104: 149 0.104 - 0.138: 27 0.138 - 0.173: 6 Chirality restraints: 1905 Sorted by residual: chirality pdb=" CA LEU B 169 " pdb=" N LEU B 169 " pdb=" C LEU B 169 " pdb=" CB LEU B 169 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.47e-01 chirality pdb=" CA LEU C 169 " pdb=" N LEU C 169 " pdb=" C LEU C 169 " pdb=" CB LEU C 169 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.42e-01 chirality pdb=" CA LEU A 169 " pdb=" N LEU A 169 " pdb=" C LEU A 169 " pdb=" CB LEU A 169 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.34e-01 ... (remaining 1902 not shown) Planarity restraints: 1944 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 323 " -0.013 2.00e-02 2.50e+03 2.58e-02 6.66e+00 pdb=" C VAL A 323 " 0.045 2.00e-02 2.50e+03 pdb=" O VAL A 323 " -0.016 2.00e-02 2.50e+03 pdb=" N TYR A 324 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 323 " -0.013 2.00e-02 2.50e+03 2.57e-02 6.63e+00 pdb=" C VAL B 323 " 0.045 2.00e-02 2.50e+03 pdb=" O VAL B 323 " -0.016 2.00e-02 2.50e+03 pdb=" N TYR B 324 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 323 " 0.013 2.00e-02 2.50e+03 2.57e-02 6.59e+00 pdb=" C VAL C 323 " -0.044 2.00e-02 2.50e+03 pdb=" O VAL C 323 " 0.016 2.00e-02 2.50e+03 pdb=" N TYR C 324 " 0.015 2.00e-02 2.50e+03 ... (remaining 1941 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 3871 2.83 - 3.35: 12256 3.35 - 3.87: 20352 3.87 - 4.38: 23969 4.38 - 4.90: 40532 Nonbonded interactions: 100980 Sorted by model distance: nonbonded pdb=" O ILE A 322 " pdb=" OG1 THR A 325 " model vdw 2.316 3.040 nonbonded pdb=" O ILE C 322 " pdb=" OG1 THR C 325 " model vdw 2.316 3.040 nonbonded pdb=" O ILE B 322 " pdb=" OG1 THR B 325 " model vdw 2.317 3.040 nonbonded pdb=" O GLY B 386 " pdb=" OG1 THR B 390 " model vdw 2.422 3.040 nonbonded pdb=" O GLY A 386 " pdb=" OG1 THR A 390 " model vdw 2.422 3.040 ... (remaining 100975 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: 0.03 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: 1.410 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: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 8.690 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 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:7.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 11928 Z= 0.285 Angle : 0.662 11.336 16266 Z= 0.394 Chirality : 0.040 0.173 1905 Planarity : 0.005 0.061 1944 Dihedral : 12.961 77.125 4023 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.23), residues: 1494 helix: 1.47 (0.15), residues: 1176 sheet: None (None), residues: 0 loop : -0.75 (0.40), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 337 TYR 0.024 0.002 TYR B 324 PHE 0.038 0.002 PHE A 193 TRP 0.011 0.001 TRP C 110 HIS 0.001 0.001 HIS C 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.29 (11928) covalent geometry : angle 0.66244 / 0.39 (16266) hydrogen bonds : bond 0.10865 / 7.22 ( 879) hydrogen bonds : angle 5.76389 / 4.08 ( 2601) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.347 Fit side-chains REVERT: A 194 MET cc_start: 0.8366 (mtp) cc_final: 0.8062 (ttm) REVERT: A 317 TYR cc_start: 0.8397 (m-80) cc_final: 0.7627 (m-80) REVERT: B 56 MET cc_start: 0.8442 (tpt) cc_final: 0.7908 (tpt) REVERT: B 194 MET cc_start: 0.8289 (mtp) cc_final: 0.7905 (ttm) REVERT: C 56 MET cc_start: 0.8438 (tpt) cc_final: 0.8119 (tpt) REVERT: C 159 TYR cc_start: 0.8546 (t80) cc_final: 0.8196 (t80) REVERT: C 317 TYR cc_start: 0.8405 (m-80) cc_final: 0.7609 (m-80) REVERT: C 447 LEU cc_start: 0.7654 (mm) cc_final: 0.7350 (mm) outliers start: 0 outliers final: 1 residues processed: 187 average time/residue: 0.3537 time to fit residues: 74.1051 Evaluate side-chains 136 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 135 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.3980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.149907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.110789 restraints weight = 12475.790| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.02 r_work: 0.2930 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11928 Z= 0.155 Angle : 0.558 5.845 16266 Z= 0.293 Chirality : 0.040 0.146 1905 Planarity : 0.004 0.036 1944 Dihedral : 4.144 19.351 1577 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.03 % Allowed : 9.02 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.22), residues: 1494 helix: 1.50 (0.15), residues: 1185 sheet: None (None), residues: 0 loop : -0.81 (0.39), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 337 TYR 0.018 0.002 TYR C 104 PHE 0.032 0.002 PHE B 240 TRP 0.012 0.001 TRP C 145 HIS 0.002 0.001 HIS A 501 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (11928) covalent geometry : angle 0.55833 / 0.29 (16266) hydrogen bonds : bond 0.04596 / 2.99 ( 879) hydrogen bonds : angle 4.82279 / 3.47 ( 2601) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 161 time to evaluate : 0.312 Fit side-chains REVERT: A 30 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.6846 (pm20) REVERT: A 317 TYR cc_start: 0.8662 (m-80) cc_final: 0.7575 (m-80) REVERT: A 448 PHE cc_start: 0.7615 (t80) cc_final: 0.7243 (t80) REVERT: B 194 MET cc_start: 0.8250 (mtp) cc_final: 0.7946 (ttm) REVERT: B 261 ILE cc_start: 0.7166 (OUTLIER) cc_final: 0.6646 (mp) REVERT: B 486 MET cc_start: 0.7991 (mtp) cc_final: 0.7784 (mtp) REVERT: C 35 LEU cc_start: 0.7296 (tt) cc_final: 0.6861 (mm) REVERT: C 56 MET cc_start: 0.8458 (tpt) cc_final: 0.8130 (tpt) REVERT: C 159 TYR cc_start: 0.8707 (t80) cc_final: 0.8373 (t80) REVERT: C 317 TYR cc_start: 0.8752 (m-80) cc_final: 0.7640 (m-80) outliers start: 25 outliers final: 13 residues processed: 170 average time/residue: 0.3217 time to fit residues: 61.8083 Evaluate side-chains 157 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 142 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 81 LYS Chi-restraints excluded: chain C residue 325 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 21 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 100 optimal weight: 10.0000 chunk 106 optimal weight: 0.4980 chunk 48 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 126 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 128 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 365 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.149791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.110079 restraints weight = 12561.401| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 1.94 r_work: 0.2880 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11928 Z= 0.149 Angle : 0.529 5.860 16266 Z= 0.279 Chirality : 0.039 0.152 1905 Planarity : 0.004 0.036 1944 Dihedral : 4.047 20.808 1577 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.76 % Allowed : 12.36 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.22), residues: 1494 helix: 1.55 (0.15), residues: 1191 sheet: None (None), residues: 0 loop : -0.60 (0.39), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 296 TYR 0.018 0.001 TYR A 104 PHE 0.031 0.002 PHE A 240 TRP 0.013 0.001 TRP C 145 HIS 0.002 0.001 HIS A 501 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (11928) covalent geometry : angle 0.52948 / 0.28 (16266) hydrogen bonds : bond 0.04353 / 2.81 ( 879) hydrogen bonds : angle 4.64645 / 3.35 ( 2601) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 154 time to evaluate : 0.318 Fit side-chains REVERT: A 30 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6788 (pm20) REVERT: A 194 MET cc_start: 0.7926 (OUTLIER) cc_final: 0.7555 (mmm) REVERT: A 317 TYR cc_start: 0.8683 (m-80) cc_final: 0.7462 (m-80) REVERT: A 448 PHE cc_start: 0.7551 (t80) cc_final: 0.7192 (t80) REVERT: B 194 MET cc_start: 0.8188 (mtp) cc_final: 0.7885 (ttm) REVERT: B 261 ILE cc_start: 0.7101 (OUTLIER) cc_final: 0.6577 (mp) REVERT: C 35 LEU cc_start: 0.7485 (tt) cc_final: 0.7089 (mm) REVERT: C 56 MET cc_start: 0.8348 (tpt) cc_final: 0.8105 (tpt) REVERT: C 159 TYR cc_start: 0.8676 (t80) cc_final: 0.8343 (t80) REVERT: C 317 TYR cc_start: 0.8759 (m-80) cc_final: 0.7869 (m-80) outliers start: 34 outliers final: 15 residues processed: 167 average time/residue: 0.2972 time to fit residues: 56.2758 Evaluate side-chains 160 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 142 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 455 ILE Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 81 LYS Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 325 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 112 optimal weight: 0.8980 chunk 61 optimal weight: 0.0970 chunk 103 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 146 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 56 optimal weight: 0.0040 chunk 78 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.151221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.111745 restraints weight = 12535.820| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.93 r_work: 0.2942 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11928 Z= 0.129 Angle : 0.509 5.905 16266 Z= 0.267 Chirality : 0.038 0.149 1905 Planarity : 0.004 0.035 1944 Dihedral : 3.955 22.584 1577 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.58 % Allowed : 12.85 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.22), residues: 1494 helix: 1.61 (0.15), residues: 1206 sheet: None (None), residues: 0 loop : -0.26 (0.41), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 337 TYR 0.017 0.001 TYR A 104 PHE 0.030 0.002 PHE A 240 TRP 0.011 0.001 TRP C 145 HIS 0.001 0.000 HIS A 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (11928) covalent geometry : angle 0.50893 / 0.27 (16266) hydrogen bonds : bond 0.04026 / 2.60 ( 879) hydrogen bonds : angle 4.57159 / 3.30 ( 2601) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 153 time to evaluate : 0.429 Fit side-chains REVERT: A 30 GLU cc_start: 0.6987 (OUTLIER) cc_final: 0.6669 (pm20) REVERT: A 194 MET cc_start: 0.7944 (OUTLIER) cc_final: 0.7600 (mmm) REVERT: A 317 TYR cc_start: 0.8691 (m-80) cc_final: 0.7441 (m-80) REVERT: A 448 PHE cc_start: 0.7597 (t80) cc_final: 0.7221 (t80) REVERT: B 30 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6684 (pm20) REVERT: B 35 LEU cc_start: 0.7200 (OUTLIER) cc_final: 0.6827 (mm) REVERT: B 194 MET cc_start: 0.8195 (mtp) cc_final: 0.7925 (ttm) REVERT: B 261 ILE cc_start: 0.7128 (OUTLIER) cc_final: 0.6612 (mp) REVERT: C 35 LEU cc_start: 0.7459 (OUTLIER) cc_final: 0.7048 (mm) REVERT: C 56 MET cc_start: 0.8308 (tpt) cc_final: 0.8033 (tpt) REVERT: C 159 TYR cc_start: 0.8683 (t80) cc_final: 0.8368 (t80) REVERT: C 261 ILE cc_start: 0.7062 (OUTLIER) cc_final: 0.6476 (mp) REVERT: C 317 TYR cc_start: 0.8800 (m-80) cc_final: 0.7975 (m-80) outliers start: 44 outliers final: 15 residues processed: 172 average time/residue: 0.3093 time to fit residues: 60.6775 Evaluate side-chains 157 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 81 LYS Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 325 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 71 optimal weight: 2.9990 chunk 122 optimal weight: 8.9990 chunk 29 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 127 optimal weight: 0.7980 chunk 144 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 89 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.150178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.110569 restraints weight = 12564.364| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.01 r_work: 0.2923 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11928 Z= 0.147 Angle : 0.522 6.066 16266 Z= 0.274 Chirality : 0.039 0.178 1905 Planarity : 0.004 0.035 1944 Dihedral : 3.944 21.539 1575 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.58 % Allowed : 13.33 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.22), residues: 1494 helix: 1.62 (0.15), residues: 1206 sheet: None (None), residues: 0 loop : -0.28 (0.41), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 337 TYR 0.018 0.001 TYR B 104 PHE 0.029 0.002 PHE A 240 TRP 0.012 0.001 TRP C 145 HIS 0.002 0.000 HIS A 501 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (11928) covalent geometry : angle 0.52171 / 0.27 (16266) hydrogen bonds : bond 0.04162 / 2.68 ( 879) hydrogen bonds : angle 4.56350 / 3.30 ( 2601) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 146 time to evaluate : 0.316 Fit side-chains REVERT: A 21 ILE cc_start: 0.7593 (OUTLIER) cc_final: 0.7336 (tt) REVERT: A 30 GLU cc_start: 0.6933 (OUTLIER) cc_final: 0.6605 (pm20) REVERT: A 194 MET cc_start: 0.7923 (OUTLIER) cc_final: 0.7589 (mmm) REVERT: A 317 TYR cc_start: 0.8714 (m-80) cc_final: 0.7536 (m-80) REVERT: A 448 PHE cc_start: 0.7678 (t80) cc_final: 0.7260 (t80) REVERT: B 30 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6654 (pm20) REVERT: B 35 LEU cc_start: 0.7100 (OUTLIER) cc_final: 0.6735 (mm) REVERT: B 194 MET cc_start: 0.8228 (mtp) cc_final: 0.7946 (ttm) REVERT: B 261 ILE cc_start: 0.7109 (OUTLIER) cc_final: 0.6594 (mp) REVERT: B 470 LEU cc_start: 0.7217 (OUTLIER) cc_final: 0.6990 (mt) REVERT: C 35 LEU cc_start: 0.7396 (OUTLIER) cc_final: 0.6985 (mm) REVERT: C 56 MET cc_start: 0.8300 (tpt) cc_final: 0.8058 (tpt) REVERT: C 159 TYR cc_start: 0.8671 (t80) cc_final: 0.8375 (t80) REVERT: C 261 ILE cc_start: 0.7019 (OUTLIER) cc_final: 0.6434 (mp) REVERT: C 317 TYR cc_start: 0.8818 (m-80) cc_final: 0.7944 (m-80) REVERT: C 451 LEU cc_start: 0.7235 (OUTLIER) cc_final: 0.6910 (mp) outliers start: 44 outliers final: 16 residues processed: 166 average time/residue: 0.3144 time to fit residues: 59.0892 Evaluate side-chains 165 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 81 LYS Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 233 LEU Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 324 TYR Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 459 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 96 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 1 optimal weight: 3.9990 chunk 93 optimal weight: 0.1980 chunk 4 optimal weight: 0.8980 chunk 22 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 129 optimal weight: 0.0970 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.151524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.112178 restraints weight = 12535.541| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.91 r_work: 0.2942 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11928 Z= 0.127 Angle : 0.502 6.061 16266 Z= 0.263 Chirality : 0.038 0.151 1905 Planarity : 0.004 0.035 1944 Dihedral : 3.864 21.769 1575 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.76 % Allowed : 15.04 % Favored : 82.20 % 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: 2.00 (0.22), residues: 1494 helix: 1.73 (0.15), residues: 1206 sheet: None (None), residues: 0 loop : -0.26 (0.41), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 337 TYR 0.017 0.001 TYR B 104 PHE 0.029 0.002 PHE B 240 TRP 0.013 0.001 TRP B 318 HIS 0.001 0.000 HIS A 501 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (11928) covalent geometry : angle 0.50158 / 0.26 (16266) hydrogen bonds : bond 0.03860 / 2.49 ( 879) hydrogen bonds : angle 4.48556 / 3.24 ( 2601) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 148 time to evaluate : 0.366 Fit side-chains REVERT: A 30 GLU cc_start: 0.6919 (OUTLIER) cc_final: 0.6508 (pm20) REVERT: A 194 MET cc_start: 0.7972 (OUTLIER) cc_final: 0.7600 (mmm) REVERT: A 317 TYR cc_start: 0.8707 (m-80) cc_final: 0.7516 (m-80) REVERT: B 30 GLU cc_start: 0.6972 (OUTLIER) cc_final: 0.6503 (pm20) REVERT: B 35 LEU cc_start: 0.7085 (OUTLIER) cc_final: 0.6718 (mm) REVERT: B 194 MET cc_start: 0.8116 (mtp) cc_final: 0.7895 (ttm) REVERT: B 261 ILE cc_start: 0.7101 (OUTLIER) cc_final: 0.6588 (mp) REVERT: B 448 PHE cc_start: 0.8256 (t80) cc_final: 0.7782 (t80) REVERT: C 35 LEU cc_start: 0.7431 (OUTLIER) cc_final: 0.7011 (mm) REVERT: C 56 MET cc_start: 0.8239 (tpt) cc_final: 0.7986 (tpt) REVERT: C 159 TYR cc_start: 0.8660 (t80) cc_final: 0.8302 (t80) REVERT: C 205 LEU cc_start: 0.7465 (mm) cc_final: 0.7232 (mt) REVERT: C 261 ILE cc_start: 0.7022 (OUTLIER) cc_final: 0.6441 (mp) REVERT: C 317 TYR cc_start: 0.8802 (m-80) cc_final: 0.7982 (m-80) REVERT: C 346 LEU cc_start: 0.7779 (tp) cc_final: 0.7491 (tp) REVERT: C 426 MET cc_start: 0.6884 (mmp) cc_final: 0.6474 (mmp) REVERT: C 451 LEU cc_start: 0.7178 (OUTLIER) cc_final: 0.6894 (mp) outliers start: 34 outliers final: 14 residues processed: 166 average time/residue: 0.3310 time to fit residues: 61.9248 Evaluate side-chains 163 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 324 TYR Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 451 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 74 optimal weight: 9.9990 chunk 126 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 56 optimal weight: 0.0030 chunk 80 optimal weight: 0.0970 chunk 25 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 136 optimal weight: 0.8980 chunk 115 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.152127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.112928 restraints weight = 12545.489| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.98 r_work: 0.2948 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11928 Z= 0.124 Angle : 0.499 6.087 16266 Z= 0.261 Chirality : 0.038 0.171 1905 Planarity : 0.004 0.034 1944 Dihedral : 3.822 21.378 1575 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.25 % Allowed : 14.80 % Favored : 81.95 % 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: 2.06 (0.22), residues: 1494 helix: 1.77 (0.15), residues: 1206 sheet: None (None), residues: 0 loop : -0.25 (0.40), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 337 TYR 0.017 0.001 TYR B 104 PHE 0.029 0.002 PHE A 240 TRP 0.013 0.001 TRP B 318 HIS 0.001 0.000 HIS A 501 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (11928) covalent geometry : angle 0.49894 / 0.26 (16266) hydrogen bonds : bond 0.03788 / 2.44 ( 879) hydrogen bonds : angle 4.45384 / 3.22 ( 2601) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 147 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 30 GLU cc_start: 0.6977 (OUTLIER) cc_final: 0.6488 (pm20) REVERT: A 194 MET cc_start: 0.7876 (OUTLIER) cc_final: 0.7458 (mmm) REVERT: A 317 TYR cc_start: 0.8700 (m-80) cc_final: 0.7512 (m-80) REVERT: A 351 TRP cc_start: 0.7567 (m100) cc_final: 0.6697 (m-10) REVERT: B 30 GLU cc_start: 0.6939 (OUTLIER) cc_final: 0.6543 (pm20) REVERT: B 35 LEU cc_start: 0.7040 (OUTLIER) cc_final: 0.6676 (mm) REVERT: B 261 ILE cc_start: 0.7070 (OUTLIER) cc_final: 0.6565 (mp) REVERT: B 448 PHE cc_start: 0.8280 (t80) cc_final: 0.7770 (t80) REVERT: C 35 LEU cc_start: 0.7402 (OUTLIER) cc_final: 0.6996 (mm) REVERT: C 56 MET cc_start: 0.8180 (tpt) cc_final: 0.7941 (tpt) REVERT: C 159 TYR cc_start: 0.8655 (t80) cc_final: 0.8311 (t80) REVERT: C 261 ILE cc_start: 0.7001 (OUTLIER) cc_final: 0.6420 (mp) REVERT: C 317 TYR cc_start: 0.8772 (m-80) cc_final: 0.7959 (m-80) REVERT: C 324 TYR cc_start: 0.8572 (OUTLIER) cc_final: 0.6746 (t80) REVERT: C 346 LEU cc_start: 0.7723 (tp) cc_final: 0.7432 (tp) REVERT: C 420 PHE cc_start: 0.7805 (OUTLIER) cc_final: 0.7262 (m-80) REVERT: C 451 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.6983 (mp) outliers start: 40 outliers final: 14 residues processed: 167 average time/residue: 0.3398 time to fit residues: 64.3783 Evaluate side-chains 165 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 141 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 324 TYR Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 420 PHE Chi-restraints excluded: chain C residue 451 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 28 optimal weight: 2.9990 chunk 143 optimal weight: 10.0000 chunk 48 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 120 optimal weight: 0.5980 chunk 121 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 61 optimal weight: 0.1980 chunk 138 optimal weight: 0.9990 chunk 141 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.151604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.112378 restraints weight = 12558.550| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.98 r_work: 0.2929 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11928 Z= 0.132 Angle : 0.529 8.824 16266 Z= 0.271 Chirality : 0.038 0.210 1905 Planarity : 0.004 0.034 1944 Dihedral : 3.845 21.084 1575 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.76 % Allowed : 15.45 % Favored : 81.79 % 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: 2.06 (0.22), residues: 1494 helix: 1.77 (0.15), residues: 1209 sheet: None (None), residues: 0 loop : -0.26 (0.40), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 337 TYR 0.017 0.001 TYR B 104 PHE 0.029 0.002 PHE A 240 TRP 0.015 0.001 TRP B 318 HIS 0.001 0.000 HIS A 501 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (11928) covalent geometry : angle 0.52857 / 0.27 (16266) hydrogen bonds : bond 0.03859 / 2.48 ( 879) hydrogen bonds : angle 4.46771 / 3.23 ( 2601) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 145 time to evaluate : 0.525 Fit side-chains REVERT: A 30 GLU cc_start: 0.6975 (OUTLIER) cc_final: 0.6474 (pm20) REVERT: A 194 MET cc_start: 0.7813 (OUTLIER) cc_final: 0.7482 (mmm) REVERT: A 233 LEU cc_start: 0.6185 (mt) cc_final: 0.5958 (mm) REVERT: A 317 TYR cc_start: 0.8726 (m-80) cc_final: 0.7558 (m-80) REVERT: A 351 TRP cc_start: 0.7618 (m100) cc_final: 0.6761 (m-10) REVERT: A 448 PHE cc_start: 0.7678 (t80) cc_final: 0.7271 (t80) REVERT: B 30 GLU cc_start: 0.6898 (OUTLIER) cc_final: 0.6447 (pm20) REVERT: B 261 ILE cc_start: 0.7100 (OUTLIER) cc_final: 0.6592 (mp) REVERT: B 346 LEU cc_start: 0.7771 (tp) cc_final: 0.7494 (tp) REVERT: B 448 PHE cc_start: 0.8258 (t80) cc_final: 0.7766 (t80) REVERT: C 35 LEU cc_start: 0.7429 (OUTLIER) cc_final: 0.7014 (mm) REVERT: C 56 MET cc_start: 0.8227 (tpt) cc_final: 0.7975 (tpt) REVERT: C 159 TYR cc_start: 0.8689 (t80) cc_final: 0.8360 (t80) REVERT: C 261 ILE cc_start: 0.7055 (OUTLIER) cc_final: 0.6469 (mp) REVERT: C 317 TYR cc_start: 0.8789 (m-80) cc_final: 0.7989 (m-80) REVERT: C 324 TYR cc_start: 0.8598 (OUTLIER) cc_final: 0.6804 (t80) REVERT: C 346 LEU cc_start: 0.7833 (tp) cc_final: 0.7529 (tp) REVERT: C 426 MET cc_start: 0.6597 (mmp) cc_final: 0.6212 (mmp) REVERT: C 451 LEU cc_start: 0.7246 (OUTLIER) cc_final: 0.6949 (mp) outliers start: 34 outliers final: 16 residues processed: 163 average time/residue: 0.3685 time to fit residues: 67.9448 Evaluate side-chains 165 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 141 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 324 TYR Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 451 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 117 optimal weight: 0.2980 chunk 103 optimal weight: 7.9990 chunk 110 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 146 optimal weight: 0.3980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.151541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.112185 restraints weight = 12527.915| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.97 r_work: 0.2949 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11928 Z= 0.134 Angle : 0.531 8.414 16266 Z= 0.271 Chirality : 0.038 0.220 1905 Planarity : 0.004 0.034 1944 Dihedral : 3.844 21.000 1575 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.52 % Allowed : 15.85 % Favored : 81.63 % 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: 2.09 (0.22), residues: 1494 helix: 1.80 (0.15), residues: 1206 sheet: None (None), residues: 0 loop : -0.26 (0.39), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 337 TYR 0.017 0.001 TYR B 104 PHE 0.029 0.002 PHE A 240 TRP 0.015 0.001 TRP B 318 HIS 0.001 0.000 HIS A 501 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (11928) covalent geometry : angle 0.53055 / 0.27 (16266) hydrogen bonds : bond 0.03889 / 2.50 ( 879) hydrogen bonds : angle 4.47906 / 3.24 ( 2601) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 144 time to evaluate : 0.348 Fit side-chains REVERT: A 30 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.6620 (pm20) REVERT: A 194 MET cc_start: 0.7862 (OUTLIER) cc_final: 0.7585 (mmm) REVERT: A 317 TYR cc_start: 0.8743 (m-80) cc_final: 0.7577 (m-80) REVERT: A 351 TRP cc_start: 0.7572 (m100) cc_final: 0.6693 (m-10) REVERT: A 448 PHE cc_start: 0.7689 (t80) cc_final: 0.7281 (t80) REVERT: B 30 GLU cc_start: 0.6903 (OUTLIER) cc_final: 0.6459 (pm20) REVERT: B 261 ILE cc_start: 0.7127 (OUTLIER) cc_final: 0.6615 (mp) REVERT: B 346 LEU cc_start: 0.7794 (tp) cc_final: 0.7511 (tp) REVERT: B 448 PHE cc_start: 0.8247 (t80) cc_final: 0.7763 (t80) REVERT: C 35 LEU cc_start: 0.7447 (OUTLIER) cc_final: 0.7023 (mm) REVERT: C 56 MET cc_start: 0.8252 (tpt) cc_final: 0.8026 (tpt) REVERT: C 159 TYR cc_start: 0.8704 (t80) cc_final: 0.8383 (t80) REVERT: C 261 ILE cc_start: 0.7084 (OUTLIER) cc_final: 0.6492 (mp) REVERT: C 317 TYR cc_start: 0.8810 (m-80) cc_final: 0.8014 (m-80) REVERT: C 324 TYR cc_start: 0.8610 (OUTLIER) cc_final: 0.6831 (t80) REVERT: C 346 LEU cc_start: 0.7865 (tp) cc_final: 0.7555 (tp) REVERT: C 451 LEU cc_start: 0.7322 (OUTLIER) cc_final: 0.7047 (mp) outliers start: 31 outliers final: 15 residues processed: 159 average time/residue: 0.3396 time to fit residues: 60.8809 Evaluate side-chains 161 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 324 TYR Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 493 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 41 optimal weight: 0.9980 chunk 54 optimal weight: 0.2980 chunk 130 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 61 optimal weight: 0.5980 chunk 75 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 120 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.151247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.111771 restraints weight = 12600.896| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.96 r_work: 0.2930 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11928 Z= 0.136 Angle : 0.537 8.390 16266 Z= 0.274 Chirality : 0.039 0.232 1905 Planarity : 0.004 0.034 1944 Dihedral : 3.851 20.658 1575 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.11 % Allowed : 16.26 % Favored : 81.63 % 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: 2.08 (0.22), residues: 1494 helix: 1.79 (0.15), residues: 1206 sheet: None (None), residues: 0 loop : -0.28 (0.39), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 446 TYR 0.018 0.001 TYR B 104 PHE 0.029 0.002 PHE A 240 TRP 0.015 0.001 TRP B 318 HIS 0.001 0.000 HIS A 501 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (11928) covalent geometry : angle 0.53738 / 0.27 (16266) hydrogen bonds : bond 0.03925 / 2.52 ( 879) hydrogen bonds : angle 4.49572 / 3.25 ( 2601) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2988 Ramachandran restraints generated. 1494 Oldfield, 0 Emsley, 1494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 146 time to evaluate : 0.418 Fit side-chains REVERT: A 30 GLU cc_start: 0.6908 (OUTLIER) cc_final: 0.6427 (pm20) REVERT: A 194 MET cc_start: 0.7664 (OUTLIER) cc_final: 0.7270 (mmm) REVERT: A 317 TYR cc_start: 0.8715 (m-80) cc_final: 0.7522 (m-80) REVERT: A 351 TRP cc_start: 0.7560 (m100) cc_final: 0.6644 (m-10) REVERT: A 448 PHE cc_start: 0.7640 (t80) cc_final: 0.7246 (t80) REVERT: B 30 GLU cc_start: 0.6907 (OUTLIER) cc_final: 0.6383 (pm20) REVERT: B 261 ILE cc_start: 0.7080 (OUTLIER) cc_final: 0.6579 (mp) REVERT: B 448 PHE cc_start: 0.8216 (t80) cc_final: 0.7717 (t80) REVERT: C 56 MET cc_start: 0.8207 (tpt) cc_final: 0.7974 (tpt) REVERT: C 159 TYR cc_start: 0.8663 (t80) cc_final: 0.8343 (t80) REVERT: C 261 ILE cc_start: 0.6999 (OUTLIER) cc_final: 0.6417 (mp) REVERT: C 317 TYR cc_start: 0.8779 (m-80) cc_final: 0.7966 (m-80) REVERT: C 324 TYR cc_start: 0.8591 (OUTLIER) cc_final: 0.6793 (t80) REVERT: C 346 LEU cc_start: 0.7803 (tp) cc_final: 0.7498 (tp) REVERT: C 451 LEU cc_start: 0.7211 (OUTLIER) cc_final: 0.6915 (mp) outliers start: 26 outliers final: 16 residues processed: 158 average time/residue: 0.3496 time to fit residues: 62.1885 Evaluate side-chains 163 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 140 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 30 GLU Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 135 TYR Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 30 GLU Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain B residue 135 TYR Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 282 MET Chi-restraints excluded: chain B residue 325 THR Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 135 TYR Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 324 TYR Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 493 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 28 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 chunk 56 optimal weight: 0.2980 chunk 76 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 84 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 135 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.151051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.111634 restraints weight = 12612.444| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.98 r_work: 0.2920 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11928 Z= 0.139 Angle : 0.541 8.354 16266 Z= 0.277 Chirality : 0.039 0.222 1905 Planarity : 0.004 0.034 1944 Dihedral : 3.863 20.703 1575 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.28 % Allowed : 16.10 % Favored : 81.63 % 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: 2.09 (0.22), residues: 1494 helix: 1.80 (0.15), residues: 1206 sheet: None (None), residues: 0 loop : -0.28 (0.39), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 337 TYR 0.018 0.001 TYR B 104 PHE 0.029 0.002 PHE A 240 TRP 0.015 0.001 TRP B 318 HIS 0.002 0.000 HIS A 501 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (11928) covalent geometry : angle 0.54110 / 0.28 (16266) hydrogen bonds : bond 0.03966 / 2.54 ( 879) hydrogen bonds : angle 4.51262 / 3.26 ( 2601) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3159.71 seconds wall clock time: 54 minutes 38.35 seconds (3278.35 seconds total)