Starting phenix.real_space_refine on Thu Aug 6 01:58:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vqt_65276/08_2026/9vqt_65276_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vqt_65276/08_2026/9vqt_65276.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vqt_65276/08_2026/9vqt_65276.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vqt_65276/08_2026/9vqt_65276.map" model { file = "/net/cci-nas-00/data/ceres_data/9vqt_65276/08_2026/9vqt_65276_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vqt_65276/08_2026/9vqt_65276_neut.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 113 5.16 5 C 8388 2.51 5 N 2024 2.21 5 O 2203 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 12728 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3097 Classifications: {'peptide': 386} Link IDs: {'PTRANS': 10, 'TRANS': 375} Chain: "B" Number of atoms: 3203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3203 Classifications: {'peptide': 402} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 394} Chain breaks: 1 Chain: "C" Number of atoms: 3203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3203 Classifications: {'peptide': 402} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 394} Chain breaks: 1 Chain: "D" Number of atoms: 3203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3203 Classifications: {'peptide': 402} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 394} Chain breaks: 1 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {' VA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.75, per 1000 atoms: 0.22 Number of scatterers: 12728 At special positions: 0 Unit cell: (118.11, 116.25, 117.18, 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 113 16.00 O 2203 8.00 N 2024 7.00 C 8388 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: 0.92 Conformation dependent library (CDL) restraints added in 464.9 milliseconds 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3026 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 3 sheets defined 81.2% alpha, 1.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 9 through 28 removed outlier: 4.065A pdb=" N CYS A 28 " --> pdb=" O PHE A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 67 Processing helix chain 'A' and resid 71 through 97 removed outlier: 4.055A pdb=" N LEU A 75 " --> pdb=" O LEU A 71 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA A 79 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N MET A 80 " --> pdb=" O GLN A 76 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL A 81 " --> pdb=" O ALA A 77 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY A 82 " --> pdb=" O MET A 78 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N SER A 83 " --> pdb=" O ALA A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 119 removed outlier: 3.938A pdb=" N GLY A 119 " --> pdb=" O TYR A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 161 removed outlier: 3.510A pdb=" N GLU A 124 " --> pdb=" O GLY A 120 " (cutoff:3.500A) Proline residue: A 143 - end of helix Proline residue: A 155 - end of helix Processing helix chain 'A' and resid 180 through 237 removed outlier: 3.685A pdb=" N GLU A 232 " --> pdb=" O LYS A 228 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 293 removed outlier: 5.400A pdb=" N ILE A 270 " --> pdb=" O ARG A 266 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N VAL A 271 " --> pdb=" O ILE A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 333 Processing helix chain 'A' and resid 335 through 339 Processing helix chain 'A' and resid 340 through 357 removed outlier: 3.858A pdb=" N ILE A 346 " --> pdb=" O LYS A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 390 Processing helix chain 'B' and resid 11 through 17 removed outlier: 3.541A pdb=" N ALA B 15 " --> pdb=" O THR B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 28 Processing helix chain 'B' and resid 38 through 67 removed outlier: 3.581A pdb=" N LYS B 42 " --> pdb=" O SER B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 97 removed outlier: 3.743A pdb=" N CYS B 87 " --> pdb=" O PHE B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 106 Processing helix chain 'B' and resid 114 through 155 removed outlier: 4.250A pdb=" N GLU B 119 " --> pdb=" O PRO B 115 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N SER B 120 " --> pdb=" O LEU B 116 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE B 155 " --> pdb=" O THR B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 244 removed outlier: 4.407A pdb=" N LYS B 239 " --> pdb=" O LYS B 235 " (cutoff:3.500A) Proline residue: B 240 - end of helix Processing helix chain 'B' and resid 324 through 378 removed outlier: 5.335A pdb=" N ALA B 357 " --> pdb=" O ASP B 353 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N ALA B 358 " --> pdb=" O THR B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 425 removed outlier: 4.120A pdb=" N PHE B 407 " --> pdb=" O HIS B 403 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N MET B 419 " --> pdb=" O SER B 415 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLU B 420 " --> pdb=" O SER B 416 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N CYS B 425 " --> pdb=" O ALA B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 446 Processing helix chain 'B' and resid 460 through 482 Processing helix chain 'C' and resid 12 through 17 Processing helix chain 'C' and resid 17 through 28 Processing helix chain 'C' and resid 38 through 67 Processing helix chain 'C' and resid 70 through 97 Processing helix chain 'C' and resid 97 through 106 Processing helix chain 'C' and resid 114 through 116 No H-bonds generated for 'chain 'C' and resid 114 through 116' Processing helix chain 'C' and resid 117 through 155 removed outlier: 3.506A pdb=" N THR C 154 " --> pdb=" O TRP C 150 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N PHE C 155 " --> pdb=" O THR C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 246 removed outlier: 3.669A pdb=" N MET C 196 " --> pdb=" O GLY C 192 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LYS C 239 " --> pdb=" O LYS C 235 " (cutoff:3.500A) Proline residue: C 240 - end of helix removed outlier: 3.703A pdb=" N SER C 245 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 379 removed outlier: 5.435A pdb=" N ALA C 357 " --> pdb=" O ASP C 353 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ALA C 358 " --> pdb=" O THR C 354 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS C 379 " --> pdb=" O TYR C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 425 removed outlier: 4.023A pdb=" N PHE C 407 " --> pdb=" O HIS C 403 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N MET C 419 " --> pdb=" O SER C 415 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLU C 420 " --> pdb=" O SER C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 445 Processing helix chain 'C' and resid 460 through 482 Processing helix chain 'D' and resid 12 through 17 Processing helix chain 'D' and resid 17 through 27 Processing helix chain 'D' and resid 38 through 67 Processing helix chain 'D' and resid 70 through 97 removed outlier: 3.844A pdb=" N CYS D 87 " --> pdb=" O PHE D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 107 Processing helix chain 'D' and resid 114 through 154 removed outlier: 4.647A pdb=" N GLU D 119 " --> pdb=" O PRO D 115 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N SER D 120 " --> pdb=" O LEU D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 246 removed outlier: 3.663A pdb=" N TYR D 195 " --> pdb=" O HIS D 191 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LYS D 239 " --> pdb=" O LYS D 235 " (cutoff:3.500A) Proline residue: D 240 - end of helix removed outlier: 3.521A pdb=" N SER D 245 " --> pdb=" O LEU D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 378 removed outlier: 5.571A pdb=" N ALA D 357 " --> pdb=" O ASP D 353 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N ALA D 358 " --> pdb=" O THR D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 417 removed outlier: 3.986A pdb=" N PHE D 407 " --> pdb=" O HIS D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 425 removed outlier: 3.971A pdb=" N CYS D 425 " --> pdb=" O ALA D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 446 Processing helix chain 'D' and resid 460 through 482 Processing sheet with id=AA1, first strand: chain 'B' and resid 160 through 165 Processing sheet with id=AA2, first strand: chain 'C' and resid 160 through 165 Processing sheet with id=AA3, first strand: chain 'D' and resid 160 through 165 1065 hydrogen bonds defined for protein. 3180 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: 1.77 Time building geometry restraints manager: 1.25 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: 1908 1.31 - 1.44: 3742 1.44 - 1.56: 7198 1.56 - 1.69: 1 1.69 - 1.81: 190 Bond restraints: 13039 Sorted by residual: bond pdb=" C20 VA A 401 " pdb=" O19 VA A 401 " ideal model delta sigma weight residual 1.328 1.409 -0.081 2.00e-02 2.50e+03 1.62e+01 bond pdb=" C12 VA A 401 " pdb=" C13 VA A 401 " ideal model delta sigma weight residual 1.497 1.559 -0.062 2.00e-02 2.50e+03 9.73e+00 bond pdb=" CA THR A 94 " pdb=" CB THR A 94 " ideal model delta sigma weight residual 1.529 1.580 -0.051 1.64e-02 3.72e+03 9.71e+00 bond pdb=" C10 VA A 401 " pdb=" C11 VA A 401 " ideal model delta sigma weight residual 1.497 1.552 -0.055 2.00e-02 2.50e+03 7.69e+00 bond pdb=" C CYS A 142 " pdb=" O CYS A 142 " ideal model delta sigma weight residual 1.244 1.227 0.017 9.40e-03 1.13e+04 3.19e+00 ... (remaining 13034 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.02: 17664 6.02 - 12.04: 1 12.04 - 18.06: 0 18.06 - 24.08: 1 24.08 - 30.10: 2 Bond angle restraints: 17668 Sorted by residual: angle pdb=" C11 VA A 401 " pdb=" C12 VA A 401 " pdb=" C13 VA A 401 " ideal model delta sigma weight residual 127.54 157.64 -30.10 3.00e+00 1.11e-01 1.01e+02 angle pdb=" C10 VA A 401 " pdb=" C11 VA A 401 " pdb=" C12 VA A 401 " ideal model delta sigma weight residual 127.47 155.98 -28.51 3.00e+00 1.11e-01 9.03e+01 angle pdb=" C12 VA A 401 " pdb=" C13 VA A 401 " pdb=" C14 VA A 401 " ideal model delta sigma weight residual 112.54 132.84 -20.30 3.00e+00 1.11e-01 4.58e+01 angle pdb=" N VAL A 168 " pdb=" CA VAL A 168 " pdb=" C VAL A 168 " ideal model delta sigma weight residual 110.42 105.67 4.75 9.60e-01 1.09e+00 2.44e+01 angle pdb=" N TYR D 355 " pdb=" CA TYR D 355 " pdb=" C TYR D 355 " ideal model delta sigma weight residual 112.88 118.15 -5.27 1.29e+00 6.01e-01 1.67e+01 ... (remaining 17663 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 6576 17.97 - 35.94: 801 35.94 - 53.91: 187 53.91 - 71.88: 28 71.88 - 89.85: 23 Dihedral angle restraints: 7615 sinusoidal: 2921 harmonic: 4694 Sorted by residual: dihedral pdb=" CA ILE A 267 " pdb=" C ILE A 267 " pdb=" N TYR A 268 " pdb=" CA TYR A 268 " ideal model delta harmonic sigma weight residual 180.00 -160.82 -19.18 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA PHE C 404 " pdb=" C PHE C 404 " pdb=" N CYS C 405 " pdb=" CA CYS C 405 " ideal model delta harmonic sigma weight residual -180.00 -162.39 -17.61 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA ASN C 77 " pdb=" CB ASN C 77 " pdb=" CG ASN C 77 " pdb=" OD1 ASN C 77 " ideal model delta sinusoidal sigma weight residual 120.00 -166.86 -73.14 2 2.00e+01 2.50e-03 1.10e+01 ... (remaining 7612 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1491 0.034 - 0.067: 408 0.067 - 0.101: 116 0.101 - 0.135: 34 0.135 - 0.168: 3 Chirality restraints: 2052 Sorted by residual: chirality pdb=" CA ILE D 176 " pdb=" N ILE D 176 " pdb=" C ILE D 176 " pdb=" CB ILE D 176 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.09e-01 chirality pdb=" CA THR A 94 " pdb=" N THR A 94 " pdb=" C THR A 94 " pdb=" CB THR A 94 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.85e-01 chirality pdb=" CA PHE C 84 " pdb=" N PHE C 84 " pdb=" C PHE C 84 " pdb=" CB PHE C 84 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.14 2.00e-01 2.50e+01 4.57e-01 ... (remaining 2049 not shown) Planarity restraints: 2134 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 102 " -0.028 2.00e-02 2.50e+03 2.02e-02 8.14e+00 pdb=" CG TYR B 102 " -0.009 2.00e-02 2.50e+03 pdb=" CD1 TYR B 102 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR B 102 " 0.037 2.00e-02 2.50e+03 pdb=" CE1 TYR B 102 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR B 102 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 102 " -0.012 2.00e-02 2.50e+03 pdb=" OH TYR B 102 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 49 " 0.012 2.00e-02 2.50e+03 2.19e-02 7.16e+00 pdb=" CG HIS B 49 " 0.002 2.00e-02 2.50e+03 pdb=" ND1 HIS B 49 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 HIS B 49 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS B 49 " 0.037 2.00e-02 2.50e+03 pdb=" NE2 HIS B 49 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 90 " 0.010 2.00e-02 2.50e+03 1.99e-02 3.95e+00 pdb=" C LYS A 90 " -0.034 2.00e-02 2.50e+03 pdb=" O LYS A 90 " 0.013 2.00e-02 2.50e+03 pdb=" N LEU A 91 " 0.012 2.00e-02 2.50e+03 ... (remaining 2131 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 319 2.70 - 3.25: 13593 3.25 - 3.80: 22417 3.80 - 4.35: 26551 4.35 - 4.90: 46561 Nonbonded interactions: 109441 Sorted by model distance: nonbonded pdb=" N GLU A 343 " pdb=" OE1 GLU A 343 " model vdw 2.147 3.120 nonbonded pdb=" O ASP A 31 " pdb=" OD1 ASP A 31 " model vdw 2.191 3.040 nonbonded pdb=" OE1 GLU B 70 " pdb=" OG SER B 171 " model vdw 2.196 3.040 nonbonded pdb=" OD2 ASP D 165 " pdb=" OG1 THR D 168 " model vdw 2.198 3.040 nonbonded pdb=" OE1 GLU D 70 " pdb=" N ASN D 72 " model vdw 2.202 3.120 ... (remaining 109436 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.090 Find NCS groups from input model: 0.150 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:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 13039 Z= 0.205 Angle : 0.644 30.105 17668 Z= 0.328 Chirality : 0.036 0.168 2052 Planarity : 0.004 0.031 2134 Dihedral : 17.028 89.849 4589 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.00 % Allowed : 21.20 % Favored : 78.80 % 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: 2.47 (0.21), residues: 1578 helix: 2.33 (0.14), residues: 1256 sheet: -1.20 (0.67), residues: 48 loop : -1.18 (0.35), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 13 TYR 0.037 0.002 TYR B 102 PHE 0.017 0.001 PHE A 171 TRP 0.008 0.001 TRP A 40 HIS 0.031 0.001 HIS B 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.20 (13039) covalent geometry : angle 0.64432 / 0.33 (17668) hydrogen bonds : bond 0.08331 / 5.76 ( 1065) hydrogen bonds : angle 4.71426 / 3.55 ( 3180) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.507 Fit side-chains REVERT: B 194 PHE cc_start: 0.6882 (m-10) cc_final: 0.6657 (m-80) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.0968 time to fit residues: 31.9305 Evaluate side-chains 213 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 232 GLN B 376 GLN C 49 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.128280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.113372 restraints weight = 17392.356| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.41 r_work: 0.3128 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.0953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13039 Z= 0.139 Angle : 0.482 9.127 17668 Z= 0.258 Chirality : 0.038 0.188 2052 Planarity : 0.003 0.034 2134 Dihedral : 4.698 58.102 1728 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 2.31 % Allowed : 19.54 % Favored : 78.15 % 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: 3.24 (0.20), residues: 1578 helix: 2.87 (0.13), residues: 1257 sheet: -0.84 (0.73), residues: 42 loop : -0.96 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 178 TYR 0.013 0.001 TYR A 115 PHE 0.021 0.001 PHE A 171 TRP 0.009 0.001 TRP A 40 HIS 0.006 0.001 HIS C 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (13039) covalent geometry : angle 0.48248 / 0.26 (17668) hydrogen bonds : bond 0.04829 / 3.27 ( 1065) hydrogen bonds : angle 3.67155 / 2.76 ( 3180) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 226 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.8197 (mmt) cc_final: 0.7921 (mmm) REVERT: B 420 GLU cc_start: 0.8215 (tp30) cc_final: 0.7506 (mp0) REVERT: D 232 GLN cc_start: 0.8598 (mm110) cc_final: 0.8360 (mm110) REVERT: D 368 ILE cc_start: 0.8178 (mm) cc_final: 0.7875 (mt) outliers start: 32 outliers final: 16 residues processed: 247 average time/residue: 0.0992 time to fit residues: 37.1236 Evaluate side-chains 221 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 205 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 198 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 39 optimal weight: 1.9990 chunk 93 optimal weight: 8.9990 chunk 124 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 116 optimal weight: 8.9990 chunk 64 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 83 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 77 ASN D 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.120853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.105551 restraints weight = 17982.582| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.46 r_work: 0.3083 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 13039 Z= 0.197 Angle : 0.522 8.184 17668 Z= 0.276 Chirality : 0.039 0.198 2052 Planarity : 0.003 0.040 2134 Dihedral : 4.406 49.341 1728 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.89 % Allowed : 19.68 % Favored : 76.42 % 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: 2.94 (0.20), residues: 1578 helix: 2.70 (0.13), residues: 1255 sheet: -1.16 (0.68), residues: 48 loop : -1.22 (0.33), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 102 TYR 0.015 0.002 TYR A 115 PHE 0.022 0.002 PHE A 171 TRP 0.010 0.001 TRP A 40 HIS 0.006 0.001 HIS C 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.20 (13039) covalent geometry : angle 0.52205 / 0.28 (17668) hydrogen bonds : bond 0.05117 / 3.47 ( 1065) hydrogen bonds : angle 3.79477 / 2.86 ( 3180) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 213 time to evaluate : 0.411 Fit side-chains revert: symmetry clash REVERT: A 165 LYS cc_start: 0.6575 (mttt) cc_final: 0.5468 (pttp) REVERT: B 420 GLU cc_start: 0.8243 (tp30) cc_final: 0.7426 (mp0) REVERT: D 55 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.7291 (mp) REVERT: D 355 TYR cc_start: 0.8634 (OUTLIER) cc_final: 0.8321 (m-80) REVERT: D 420 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8010 (mt-10) outliers start: 54 outliers final: 36 residues processed: 250 average time/residue: 0.0926 time to fit residues: 35.1186 Evaluate side-chains 239 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 200 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 208 TYR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 196 MET Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 355 TYR Chi-restraints excluded: chain D residue 366 SER Chi-restraints excluded: chain D residue 420 GLU Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 480 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 90 optimal weight: 0.9980 chunk 81 optimal weight: 7.9990 chunk 126 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 chunk 147 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 chunk 5 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 232 GLN ** C 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.122845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.107424 restraints weight = 17831.901| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.47 r_work: 0.3118 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13039 Z= 0.138 Angle : 0.463 8.043 17668 Z= 0.247 Chirality : 0.037 0.177 2052 Planarity : 0.003 0.042 2134 Dihedral : 4.172 42.980 1728 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 3.32 % Allowed : 20.69 % Favored : 75.99 % 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: 3.16 (0.20), residues: 1578 helix: 2.86 (0.13), residues: 1257 sheet: -1.23 (0.66), residues: 48 loop : -1.19 (0.33), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 22 TYR 0.013 0.001 TYR D 355 PHE 0.019 0.001 PHE A 171 TRP 0.009 0.001 TRP A 40 HIS 0.006 0.001 HIS C 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (13039) covalent geometry : angle 0.46336 / 0.25 (17668) hydrogen bonds : bond 0.04758 / 3.22 ( 1065) hydrogen bonds : angle 3.63580 / 2.74 ( 3180) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 220 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.8041 (mmp) cc_final: 0.7704 (mmt) REVERT: A 101 LEU cc_start: 0.9043 (tt) cc_final: 0.8821 (tt) REVERT: B 110 GLN cc_start: 0.8354 (mm-40) cc_final: 0.8140 (mm-40) REVERT: B 420 GLU cc_start: 0.8176 (tp30) cc_final: 0.7401 (mp0) REVERT: C 394 LEU cc_start: 0.8805 (mt) cc_final: 0.8496 (mt) REVERT: D 31 MET cc_start: 0.8424 (tpp) cc_final: 0.7800 (tpp) REVERT: D 55 LEU cc_start: 0.7429 (OUTLIER) cc_final: 0.7199 (mp) REVERT: D 355 TYR cc_start: 0.8583 (OUTLIER) cc_final: 0.8029 (m-80) REVERT: D 420 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.7999 (mt-10) outliers start: 46 outliers final: 27 residues processed: 252 average time/residue: 0.0991 time to fit residues: 38.1219 Evaluate side-chains 233 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 203 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 208 TYR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 196 MET Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 355 TYR Chi-restraints excluded: chain D residue 366 SER Chi-restraints excluded: chain D residue 420 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 66 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 80 optimal weight: 0.0010 chunk 97 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 152 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 overall best weight: 1.9994 ------------------------------------------------------------------------------- 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 = 0.3396 r_free = 0.3396 target = 0.121210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.105688 restraints weight = 18086.016| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.51 r_work: 0.3098 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13039 Z= 0.165 Angle : 0.488 8.055 17668 Z= 0.260 Chirality : 0.038 0.177 2052 Planarity : 0.003 0.044 2134 Dihedral : 4.242 43.016 1728 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 3.68 % Allowed : 21.41 % Favored : 74.91 % 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: 3.00 (0.20), residues: 1578 helix: 2.74 (0.13), residues: 1257 sheet: -1.34 (0.65), residues: 48 loop : -1.20 (0.33), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 22 TYR 0.014 0.001 TYR A 115 PHE 0.022 0.001 PHE A 171 TRP 0.009 0.001 TRP A 40 HIS 0.005 0.001 HIS C 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 (13039) covalent geometry : angle 0.48809 / 0.26 (17668) hydrogen bonds : bond 0.04908 / 3.32 ( 1065) hydrogen bonds : angle 3.71105 / 2.79 ( 3180) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 212 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.8058 (mmp) cc_final: 0.7658 (tpp) REVERT: B 90 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8401 (mmtp) REVERT: B 110 GLN cc_start: 0.8398 (mm-40) cc_final: 0.8176 (mm-40) REVERT: B 420 GLU cc_start: 0.8194 (tp30) cc_final: 0.7353 (mp0) REVERT: C 417 SER cc_start: 0.7953 (p) cc_final: 0.7583 (m) REVERT: D 31 MET cc_start: 0.8422 (tpp) cc_final: 0.7982 (tpp) REVERT: D 55 LEU cc_start: 0.7457 (OUTLIER) cc_final: 0.7218 (mp) REVERT: D 232 GLN cc_start: 0.8810 (mm110) cc_final: 0.8522 (mm110) REVERT: D 355 TYR cc_start: 0.8596 (OUTLIER) cc_final: 0.8233 (m-80) REVERT: D 420 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8049 (mt-10) outliers start: 51 outliers final: 32 residues processed: 249 average time/residue: 0.0854 time to fit residues: 32.3745 Evaluate side-chains 235 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 199 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 208 TYR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 196 MET Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 355 TYR Chi-restraints excluded: chain D residue 366 SER Chi-restraints excluded: chain D residue 420 GLU Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 480 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 37 optimal weight: 0.9980 chunk 156 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 87 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 68 optimal weight: 0.0670 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 480 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.130459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.115537 restraints weight = 17456.633| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.42 r_work: 0.3166 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13039 Z= 0.115 Angle : 0.448 7.898 17668 Z= 0.237 Chirality : 0.036 0.150 2052 Planarity : 0.003 0.044 2134 Dihedral : 4.022 38.682 1728 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 3.10 % Allowed : 21.92 % Favored : 74.98 % 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: 3.43 (0.20), residues: 1578 helix: 3.02 (0.13), residues: 1257 sheet: -1.00 (0.68), residues: 42 loop : -0.98 (0.34), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 123 TYR 0.018 0.001 TYR D 45 PHE 0.024 0.001 PHE B 184 TRP 0.008 0.001 TRP A 41 HIS 0.006 0.001 HIS C 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (13039) covalent geometry : angle 0.44819 / 0.24 (17668) hydrogen bonds : bond 0.04506 / 3.04 ( 1065) hydrogen bonds : angle 3.54849 / 2.67 ( 3180) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 224 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.7882 (mmp) cc_final: 0.7558 (tpp) REVERT: B 90 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8439 (mmtp) REVERT: B 110 GLN cc_start: 0.8337 (mm-40) cc_final: 0.8113 (mm-40) REVERT: B 353 ASP cc_start: 0.7644 (m-30) cc_final: 0.7436 (m-30) REVERT: B 420 GLU cc_start: 0.8142 (tp30) cc_final: 0.7510 (mp0) REVERT: C 394 LEU cc_start: 0.8800 (mt) cc_final: 0.8156 (mt) REVERT: C 417 SER cc_start: 0.7878 (p) cc_final: 0.7505 (m) REVERT: D 55 LEU cc_start: 0.7399 (OUTLIER) cc_final: 0.7154 (mp) REVERT: D 196 MET cc_start: 0.5365 (OUTLIER) cc_final: 0.5118 (mtt) REVERT: D 232 GLN cc_start: 0.8808 (mm110) cc_final: 0.8484 (mm110) REVERT: D 355 TYR cc_start: 0.8474 (OUTLIER) cc_final: 0.7479 (m-80) REVERT: D 368 ILE cc_start: 0.8206 (mm) cc_final: 0.7923 (mt) REVERT: D 414 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7501 (mm-30) REVERT: D 420 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7986 (mt-10) outliers start: 43 outliers final: 29 residues processed: 254 average time/residue: 0.0915 time to fit residues: 35.1597 Evaluate side-chains 243 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 209 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 208 TYR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain A residue 359 TYR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 204 TYR Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 86 HIS Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 196 MET Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 204 TYR Chi-restraints excluded: chain D residue 343 HIS Chi-restraints excluded: chain D residue 355 TYR Chi-restraints excluded: chain D residue 420 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 93 optimal weight: 9.9990 chunk 121 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 142 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 chunk 131 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 = 0.3506 r_free = 0.3506 target = 0.128925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.114204 restraints weight = 17357.102| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.39 r_work: 0.3119 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13039 Z= 0.166 Angle : 0.498 7.912 17668 Z= 0.262 Chirality : 0.038 0.161 2052 Planarity : 0.003 0.045 2134 Dihedral : 4.194 42.384 1728 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 3.39 % Allowed : 22.06 % Favored : 74.55 % 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: 3.14 (0.20), residues: 1578 helix: 2.84 (0.13), residues: 1257 sheet: -1.30 (0.63), residues: 48 loop : -1.12 (0.33), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 123 TYR 0.014 0.001 TYR A 115 PHE 0.021 0.001 PHE A 171 TRP 0.008 0.001 TRP A 40 HIS 0.005 0.001 HIS C 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 (13039) covalent geometry : angle 0.49806 / 0.26 (17668) hydrogen bonds : bond 0.04834 / 3.27 ( 1065) hydrogen bonds : angle 3.67163 / 2.76 ( 3180) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 211 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.7910 (mmp) cc_final: 0.7627 (tpp) REVERT: B 90 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8402 (mmtp) REVERT: B 420 GLU cc_start: 0.8185 (tp30) cc_final: 0.7533 (mp0) REVERT: C 417 SER cc_start: 0.7937 (p) cc_final: 0.7539 (m) REVERT: D 55 LEU cc_start: 0.7450 (OUTLIER) cc_final: 0.7201 (mp) REVERT: D 232 GLN cc_start: 0.8829 (mm110) cc_final: 0.8533 (mm110) REVERT: D 355 TYR cc_start: 0.8562 (OUTLIER) cc_final: 0.8175 (m-80) REVERT: D 414 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7553 (mm-30) REVERT: D 420 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8058 (mt-10) outliers start: 47 outliers final: 36 residues processed: 244 average time/residue: 0.0957 time to fit residues: 34.9344 Evaluate side-chains 244 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 204 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 208 TYR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 90 LYS Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 196 MET Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 355 TYR Chi-restraints excluded: chain D residue 366 SER Chi-restraints excluded: chain D residue 388 PHE Chi-restraints excluded: chain D residue 420 GLU Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain D residue 480 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 8 optimal weight: 0.6980 chunk 146 optimal weight: 2.9990 chunk 93 optimal weight: 9.9990 chunk 2 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 chunk 136 optimal weight: 7.9990 chunk 33 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3451 r_free = 0.3451 target = 0.125556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.110205 restraints weight = 17665.743| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.44 r_work: 0.3145 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13039 Z= 0.126 Angle : 0.469 7.842 17668 Z= 0.247 Chirality : 0.036 0.153 2052 Planarity : 0.003 0.045 2134 Dihedral : 4.066 39.273 1728 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 2.96 % Allowed : 22.21 % Favored : 74.84 % 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: 3.41 (0.20), residues: 1578 helix: 2.99 (0.13), residues: 1257 sheet: -0.97 (0.67), residues: 42 loop : -0.90 (0.34), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 123 TYR 0.017 0.001 TYR D 45 PHE 0.022 0.001 PHE D 475 TRP 0.008 0.001 TRP A 40 HIS 0.006 0.001 HIS C 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (13039) covalent geometry : angle 0.46901 / 0.25 (17668) hydrogen bonds : bond 0.04591 / 3.10 ( 1065) hydrogen bonds : angle 3.57278 / 2.69 ( 3180) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 219 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.7824 (mmp) cc_final: 0.7594 (tpp) REVERT: A 178 GLU cc_start: 0.7894 (pt0) cc_final: 0.6444 (tm-30) REVERT: B 420 GLU cc_start: 0.8170 (tp30) cc_final: 0.7511 (mp0) REVERT: C 375 TYR cc_start: 0.7989 (t80) cc_final: 0.7760 (t80) REVERT: C 394 LEU cc_start: 0.8804 (mt) cc_final: 0.8484 (mt) REVERT: C 417 SER cc_start: 0.7919 (p) cc_final: 0.7537 (m) REVERT: D 55 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.7143 (mp) REVERT: D 232 GLN cc_start: 0.8800 (mm110) cc_final: 0.8597 (mm-40) REVERT: D 355 TYR cc_start: 0.8522 (OUTLIER) cc_final: 0.7579 (m-80) REVERT: D 368 ILE cc_start: 0.8208 (mm) cc_final: 0.7929 (mt) REVERT: D 420 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8042 (mt-10) outliers start: 41 outliers final: 32 residues processed: 247 average time/residue: 0.1003 time to fit residues: 37.0987 Evaluate side-chains 244 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 209 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 208 TYR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain A residue 359 TYR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 355 TYR Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 86 HIS Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 196 MET Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 204 TYR Chi-restraints excluded: chain D residue 343 HIS Chi-restraints excluded: chain D residue 355 TYR Chi-restraints excluded: chain D residue 420 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 56 optimal weight: 0.0980 chunk 28 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 chunk 128 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 chunk 136 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 480 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.123695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.108414 restraints weight = 17785.291| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.44 r_work: 0.3117 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13039 Z= 0.157 Angle : 0.496 7.870 17668 Z= 0.261 Chirality : 0.038 0.153 2052 Planarity : 0.003 0.045 2134 Dihedral : 4.180 41.325 1728 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 3.32 % Allowed : 22.28 % Favored : 74.41 % 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: 3.17 (0.20), residues: 1578 helix: 2.85 (0.13), residues: 1257 sheet: -1.38 (0.63), residues: 48 loop : -1.07 (0.33), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 123 TYR 0.014 0.001 TYR A 115 PHE 0.022 0.001 PHE D 475 TRP 0.008 0.001 TRP A 40 HIS 0.005 0.001 HIS C 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (13039) covalent geometry : angle 0.49581 / 0.26 (17668) hydrogen bonds : bond 0.04788 / 3.24 ( 1065) hydrogen bonds : angle 3.66607 / 2.76 ( 3180) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 211 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.7838 (mmp) cc_final: 0.7609 (tpp) REVERT: A 178 GLU cc_start: 0.7850 (pt0) cc_final: 0.6261 (tm-30) REVERT: A 239 GLU cc_start: 0.6946 (tp30) cc_final: 0.6620 (tp30) REVERT: B 353 ASP cc_start: 0.7630 (m-30) cc_final: 0.7368 (m-30) REVERT: B 420 GLU cc_start: 0.8202 (tp30) cc_final: 0.7531 (mp0) REVERT: C 417 SER cc_start: 0.7948 (p) cc_final: 0.7558 (m) REVERT: D 55 LEU cc_start: 0.7411 (OUTLIER) cc_final: 0.7154 (mp) REVERT: D 232 GLN cc_start: 0.8820 (mm110) cc_final: 0.8587 (mm-40) REVERT: D 355 TYR cc_start: 0.8575 (OUTLIER) cc_final: 0.8122 (m-80) REVERT: D 420 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8062 (mt-10) outliers start: 46 outliers final: 38 residues processed: 243 average time/residue: 0.1045 time to fit residues: 37.9354 Evaluate side-chains 246 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 205 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 208 TYR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 86 HIS Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 196 MET Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 343 HIS Chi-restraints excluded: chain D residue 355 TYR Chi-restraints excluded: chain D residue 366 SER Chi-restraints excluded: chain D residue 420 GLU Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 467 VAL Chi-restraints excluded: chain D residue 480 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 11 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 chunk 93 optimal weight: 10.0000 chunk 155 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 116 optimal weight: 0.7980 chunk 134 optimal weight: 0.0980 chunk 146 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3447 r_free = 0.3447 target = 0.125016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.109671 restraints weight = 17870.511| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.45 r_work: 0.3118 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 13039 Z= 0.147 Angle : 0.773 59.164 17668 Z= 0.441 Chirality : 0.037 0.155 2052 Planarity : 0.003 0.045 2134 Dihedral : 4.176 41.181 1728 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.81 % Allowed : 22.78 % Favored : 74.41 % Cbeta Deviations : 0.07 % 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: 3.19 (0.20), residues: 1578 helix: 2.87 (0.13), residues: 1257 sheet: -1.38 (0.63), residues: 48 loop : -1.07 (0.33), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 123 TYR 0.016 0.001 TYR D 102 PHE 0.020 0.001 PHE A 171 TRP 0.009 0.001 TRP C 337 HIS 0.005 0.001 HIS C 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 (13039) covalent geometry : angle 0.77263 / 0.44 (17668) hydrogen bonds : bond 0.04771 / 3.24 ( 1065) hydrogen bonds : angle 3.66345 / 2.76 ( 3180) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 206 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.7845 (mmp) cc_final: 0.7612 (tpp) REVERT: A 178 GLU cc_start: 0.7838 (pt0) cc_final: 0.6239 (tm-30) REVERT: B 353 ASP cc_start: 0.7635 (m-30) cc_final: 0.7373 (m-30) REVERT: B 420 GLU cc_start: 0.8209 (tp30) cc_final: 0.7515 (mp0) REVERT: C 417 SER cc_start: 0.7941 (p) cc_final: 0.7554 (m) REVERT: D 55 LEU cc_start: 0.7403 (OUTLIER) cc_final: 0.7152 (mp) REVERT: D 232 GLN cc_start: 0.8825 (mm110) cc_final: 0.8587 (mm-40) REVERT: D 355 TYR cc_start: 0.8552 (OUTLIER) cc_final: 0.8106 (m-80) REVERT: D 420 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8070 (mt-10) outliers start: 39 outliers final: 36 residues processed: 235 average time/residue: 0.1062 time to fit residues: 37.4815 Evaluate side-chains 245 residues out of total 1387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 206 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 MET Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 208 TYR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 378 THR Chi-restraints excluded: chain B residue 438 VAL Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 165 ASP Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 355 TYR Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 49 HIS Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 86 HIS Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 196 MET Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 343 HIS Chi-restraints excluded: chain D residue 355 TYR Chi-restraints excluded: chain D residue 366 SER Chi-restraints excluded: chain D residue 420 GLU Chi-restraints excluded: chain D residue 467 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 101 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 152 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 97 optimal weight: 5.9990 chunk 62 optimal weight: 0.4980 chunk 16 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3433 r_free = 0.3433 target = 0.124083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.108697 restraints weight = 17760.268| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.44 r_work: 0.3121 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 13039 Z= 0.147 Angle : 0.773 59.164 17668 Z= 0.441 Chirality : 0.037 0.155 2052 Planarity : 0.003 0.045 2134 Dihedral : 4.176 41.181 1728 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.81 % Allowed : 22.78 % Favored : 74.41 % Cbeta Deviations : 0.07 % 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: 3.19 (0.20), residues: 1578 helix: 2.87 (0.13), residues: 1257 sheet: -1.38 (0.63), residues: 48 loop : -1.07 (0.33), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 123 TYR 0.016 0.001 TYR D 102 PHE 0.020 0.001 PHE A 171 TRP 0.009 0.001 TRP C 337 HIS 0.005 0.001 HIS C 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 (13039) covalent geometry : angle 0.77263 / 0.44 (17668) hydrogen bonds : bond 0.04771 / 3.24 ( 1065) hydrogen bonds : angle 3.66345 / 2.76 ( 3180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3038.28 seconds wall clock time: 53 minutes 12.67 seconds (3192.67 seconds total)