Starting phenix.real_space_refine on Tue Mar 3 20:08:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z2d_14462/03_2026/7z2d_14462.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z2d_14462/03_2026/7z2d_14462.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7z2d_14462/03_2026/7z2d_14462.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z2d_14462/03_2026/7z2d_14462.map" model { file = "/net/cci-nas-00/data/ceres_data/7z2d_14462/03_2026/7z2d_14462.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z2d_14462/03_2026/7z2d_14462.cif" } resolution = 3.38 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= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 35 5.49 5 S 13 5.16 5 C 5452 2.51 5 N 1432 2.21 5 O 1659 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8591 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4450 Classifications: {'peptide': 547} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 36, 'TRANS': 508} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3393 Classifications: {'peptide': 412} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 30, 'TRANS': 381} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 720 Classifications: {'DNA': 34, 'RNA': 2} Modifications used: {'5*END': 1, 'rna3p': 2} Link IDs: {'rna3p': 35} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DA%5*END:plan': 1, ' DA%5*END:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'T27': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.67, per 1000 atoms: 0.19 Number of scatterers: 8591 At special positions: 0 Unit cell: (97, 109.61, 100.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 13 16.00 P 35 15.00 O 1659 8.00 N 1432 7.00 C 5452 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: 0.67 Conformation dependent library (CDL) restraints added in 259.1 milliseconds 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1804 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 8 sheets defined 38.0% alpha, 13.0% beta 9 base pairs and 29 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 33 through 44 Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 96 through 100 Processing helix chain 'A' and resid 112 through 117 removed outlier: 3.622A pdb=" N TYR A 115 " --> pdb=" O GLY A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 128 removed outlier: 3.688A pdb=" N THR A 128 " --> pdb=" O ARG A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 175 Proline residue: A 170 - end of helix removed outlier: 3.741A pdb=" N GLN A 174 " --> pdb=" O PRO A 170 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN A 175 " --> pdb=" O PHE A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 212 removed outlier: 3.869A pdb=" N ARG A 199 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N THR A 200 " --> pdb=" O GLY A 196 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS A 201 " --> pdb=" O GLN A 197 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TRP A 212 " --> pdb=" O HIS A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 224 removed outlier: 3.937A pdb=" N LYS A 223 " --> pdb=" O LYS A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 268 Processing helix chain 'A' and resid 276 through 281 removed outlier: 3.787A pdb=" N LYS A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 284 No H-bonds generated for 'chain 'A' and resid 282 through 284' Processing helix chain 'A' and resid 296 through 311 removed outlier: 3.637A pdb=" N ILE A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU A 310 " --> pdb=" O ASN A 306 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LYS A 311 " --> pdb=" O ARG A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 383 removed outlier: 3.568A pdb=" N GLN A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS A 374 " --> pdb=" O GLU A 370 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE A 375 " --> pdb=" O ALA A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 403 Processing helix chain 'A' and resid 473 through 488 removed outlier: 3.702A pdb=" N ASP A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 508 removed outlier: 3.928A pdb=" N LEU A 503 " --> pdb=" O SER A 499 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA A 508 " --> pdb=" O GLY A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 528 removed outlier: 3.894A pdb=" N LYS A 527 " --> pdb=" O GLU A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 554 Processing helix chain 'B' and resid 27 through 43 removed outlier: 3.793A pdb=" N LEU B 34 " --> pdb=" O LYS B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 84 Processing helix chain 'B' and resid 84 through 91 removed outlier: 4.149A pdb=" N TRP B 88 " --> pdb=" O THR B 84 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU B 89 " --> pdb=" O GLN B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 116 Processing helix chain 'B' and resid 121 through 125 removed outlier: 3.552A pdb=" N ARG B 125 " --> pdb=" O GLU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 138 Processing helix chain 'B' and resid 154 through 175 removed outlier: 3.893A pdb=" N ALA B 158 " --> pdb=" O LYS B 154 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N SER B 162 " --> pdb=" O ALA B 158 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N SER B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS B 166 " --> pdb=" O SER B 162 " (cutoff:3.500A) Proline residue: B 170 - end of helix Processing helix chain 'B' and resid 194 through 213 Processing helix chain 'B' and resid 235 through 239 Processing helix chain 'B' and resid 253 through 268 Processing helix chain 'B' and resid 277 through 283 removed outlier: 3.581A pdb=" N LEU B 282 " --> pdb=" O LEU B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 310 Processing helix chain 'B' and resid 364 through 383 Processing helix chain 'B' and resid 394 through 402 Processing helix chain 'B' and resid 403 through 405 No H-bonds generated for 'chain 'B' and resid 403 through 405' Processing sheet with id=AA1, first strand: chain 'A' and resid 105 through 110 Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 354 removed outlier: 7.643A pdb=" N LYS A 347 " --> pdb=" O GLN A 343 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLN A 343 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE A 341 " --> pdb=" O LEU A 349 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N THR A 351 " --> pdb=" O TYR A 339 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N TYR A 339 " --> pdb=" O THR A 351 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LYS A 353 " --> pdb=" O TRP A 337 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N TRP A 337 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE A 329 " --> pdb=" O LYS A 390 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 361 through 362 Processing sheet with id=AA4, first strand: chain 'A' and resid 464 through 470 Processing sheet with id=AA5, first strand: chain 'B' and resid 47 through 49 Processing sheet with id=AA6, first strand: chain 'B' and resid 60 through 65 removed outlier: 4.431A pdb=" N LYS B 65 " --> pdb=" O LYS B 70 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LYS B 70 " --> pdb=" O LYS B 65 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 179 through 183 Processing sheet with id=AA8, first strand: chain 'B' and resid 347 through 354 removed outlier: 8.273A pdb=" N ASN B 348 " --> pdb=" O GLN B 343 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N GLN B 343 " --> pdb=" O ASN B 348 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N GLN B 336 " --> pdb=" O GLN B 332 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN B 340 " --> pdb=" O GLU B 328 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU B 328 " --> pdb=" O GLN B 340 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ILE B 329 " --> pdb=" O LYS B 390 " (cutoff:3.500A) 288 hydrogen bonds defined for protein. 783 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 24 hydrogen bonds 48 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 29 stacking parallelities Total time for adding SS restraints: 1.34 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1342 1.27 - 1.40: 2187 1.40 - 1.54: 5116 1.54 - 1.67: 220 1.67 - 1.81: 25 Bond restraints: 8890 Sorted by residual: bond pdb=" O3' DC E 3 " pdb=" P OMC E 4 " ideal model delta sigma weight residual 1.607 1.700 -0.093 1.50e-02 4.44e+03 3.81e+01 bond pdb=" C20 T27 A 601 " pdb=" C22 T27 A 601 " ideal model delta sigma weight residual 1.419 1.525 -0.106 2.00e-02 2.50e+03 2.83e+01 bond pdb=" C13 T27 A 601 " pdb=" C19 T27 A 601 " ideal model delta sigma weight residual 1.422 1.524 -0.102 2.00e-02 2.50e+03 2.62e+01 bond pdb=" C11 T27 A 601 " pdb=" N1 T27 A 601 " ideal model delta sigma weight residual 1.351 1.453 -0.102 2.00e-02 2.50e+03 2.61e+01 bond pdb=" C12 T27 A 601 " pdb=" N4 T27 A 601 " ideal model delta sigma weight residual 1.372 1.455 -0.083 2.00e-02 2.50e+03 1.74e+01 ... (remaining 8885 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.98: 12126 2.98 - 5.95: 96 5.95 - 8.93: 7 8.93 - 11.91: 1 11.91 - 14.88: 1 Bond angle restraints: 12231 Sorted by residual: angle pdb=" C5' DA E 25 " pdb=" C4' DA E 25 " pdb=" O4' DA E 25 " ideal model delta sigma weight residual 109.40 116.92 -7.52 1.50e+00 4.44e-01 2.51e+01 angle pdb=" C2 T27 A 601 " pdb=" C1 T27 A 601 " pdb=" C7 T27 A 601 " ideal model delta sigma weight residual 120.40 105.52 14.88 3.00e+00 1.11e-01 2.46e+01 angle pdb=" C6 T27 A 601 " pdb=" C1 T27 A 601 " pdb=" C7 T27 A 601 " ideal model delta sigma weight residual 121.15 131.96 -10.81 3.00e+00 1.11e-01 1.30e+01 angle pdb=" C3' OMC E 4 " pdb=" C2' OMC E 4 " pdb=" C1' OMC E 4 " ideal model delta sigma weight residual 101.30 104.74 -3.44 1.00e+00 1.00e+00 1.19e+01 angle pdb=" C12 T27 A 601 " pdb=" N4 T27 A 601 " pdb=" C16 T27 A 601 " ideal model delta sigma weight residual 131.80 123.10 8.70 3.00e+00 1.11e-01 8.41e+00 ... (remaining 12226 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 4482 17.84 - 35.68: 569 35.68 - 53.52: 111 53.52 - 71.36: 37 71.36 - 89.20: 9 Dihedral angle restraints: 5208 sinusoidal: 2410 harmonic: 2798 Sorted by residual: dihedral pdb=" CA PRO B 4 " pdb=" CB PRO B 4 " pdb=" CG PRO B 4 " pdb=" CD PRO B 4 " ideal model delta sinusoidal sigma weight residual 38.00 115.32 -77.32 1 2.00e+01 2.50e-03 1.87e+01 dihedral pdb=" CA GLU A 224 " pdb=" C GLU A 224 " pdb=" N PRO A 225 " pdb=" CA PRO A 225 " ideal model delta harmonic sigma weight residual 180.00 160.54 19.46 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA ILE A 309 " pdb=" C ILE A 309 " pdb=" N LEU A 310 " pdb=" CA LEU A 310 " ideal model delta harmonic sigma weight residual -180.00 -161.65 -18.35 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 5205 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1189 0.075 - 0.150: 138 0.150 - 0.225: 1 0.225 - 0.300: 0 0.300 - 0.375: 1 Chirality restraints: 1329 Sorted by residual: chirality pdb=" C4' DA E 25 " pdb=" C5' DA E 25 " pdb=" O4' DA E 25 " pdb=" C3' DA E 25 " both_signs ideal model delta sigma weight residual False -2.53 -2.15 -0.37 2.00e-01 2.50e+01 3.51e+00 chirality pdb=" C3' DT E 8 " pdb=" C4' DT E 8 " pdb=" O3' DT E 8 " pdb=" C2' DT E 8 " both_signs ideal model delta sigma weight residual False -2.66 -2.47 -0.19 2.00e-01 2.50e+01 9.34e-01 chirality pdb=" CA ILE B 180 " pdb=" N ILE B 180 " pdb=" C ILE B 180 " pdb=" CB ILE B 180 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.31e-01 ... (remaining 1326 not shown) Planarity restraints: 1421 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 420 " 0.046 5.00e-02 4.00e+02 6.98e-02 7.79e+00 pdb=" N PRO A 421 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO A 421 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 421 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 18 " -0.038 5.00e-02 4.00e+02 5.83e-02 5.44e+00 pdb=" N PRO A 19 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 19 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 19 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 467 " -0.031 5.00e-02 4.00e+02 4.68e-02 3.50e+00 pdb=" N PRO A 468 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 468 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 468 " -0.026 5.00e-02 4.00e+02 ... (remaining 1418 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 454 2.73 - 3.27: 7951 3.27 - 3.81: 13893 3.81 - 4.36: 16752 4.36 - 4.90: 28425 Nonbonded interactions: 67475 Sorted by model distance: nonbonded pdb=" NH2 ARG B 356 " pdb=" O ALA B 360 " model vdw 2.187 3.120 nonbonded pdb=" OH TYR B 354 " pdb=" OE2 GLU B 378 " model vdw 2.196 3.040 nonbonded pdb=" NZ LYS B 73 " pdb=" OH TYR B 146 " model vdw 2.216 3.120 nonbonded pdb=" NZ LYS B 366 " pdb=" OE2 GLU B 370 " model vdw 2.221 3.120 nonbonded pdb=" OE2 GLU A 328 " pdb=" OH TYR A 342 " model vdw 2.229 3.040 ... (remaining 67470 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.120 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.250 Find NCS groups from input model: 0.040 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6733 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 0.106 8890 Z= 0.217 Angle : 0.662 14.883 12231 Z= 0.342 Chirality : 0.044 0.375 1329 Planarity : 0.005 0.070 1421 Dihedral : 16.348 89.196 3404 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.28), residues: 951 helix: 1.36 (0.32), residues: 307 sheet: 0.11 (0.42), residues: 157 loop : -0.97 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 83 TYR 0.013 0.001 TYR A 319 PHE 0.010 0.001 PHE B 130 TRP 0.019 0.001 TRP A 402 HIS 0.006 0.001 HIS B 208 Details of bonding type rmsd covalent geometry : bond 0.00444 ( 8890) covalent geometry : angle 0.66176 (12231) hydrogen bonds : bond 0.13935 ( 312) hydrogen bonds : angle 5.84384 ( 831) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.299 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.0915 time to fit residues: 15.2742 Evaluate side-chains 96 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 40.0000 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 GLN B 54 ASN B 182 GLN B 207 GLN B 367 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.213531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.176095 restraints weight = 9540.249| |-----------------------------------------------------------------------------| r_work (start): 0.4048 rms_B_bonded: 2.05 r_work: 0.3779 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8890 Z= 0.183 Angle : 0.595 6.270 12231 Z= 0.307 Chirality : 0.043 0.145 1329 Planarity : 0.005 0.060 1421 Dihedral : 14.709 84.585 1377 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 1.40 % Allowed : 6.75 % Favored : 91.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.28), residues: 951 helix: 1.10 (0.30), residues: 321 sheet: -0.37 (0.40), residues: 168 loop : -0.97 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 358 TYR 0.018 0.002 TYR B 144 PHE 0.011 0.002 PHE B 130 TRP 0.018 0.002 TRP A 402 HIS 0.004 0.001 HIS B 208 Details of bonding type rmsd covalent geometry : bond 0.00433 ( 8890) covalent geometry : angle 0.59504 (12231) hydrogen bonds : bond 0.04138 ( 312) hydrogen bonds : angle 4.33629 ( 831) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.282 Fit side-chains REVERT: A 516 GLU cc_start: 0.6634 (tp30) cc_final: 0.5548 (pm20) outliers start: 12 outliers final: 6 residues processed: 114 average time/residue: 0.0937 time to fit residues: 14.7184 Evaluate side-chains 104 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 98 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 131 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 26 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 chunk 73 optimal weight: 7.9990 chunk 6 optimal weight: 20.0000 chunk 10 optimal weight: 5.9990 chunk 64 optimal weight: 30.0000 chunk 66 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 54 optimal weight: 8.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 500 GLN B 367 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.211765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.174762 restraints weight = 9604.357| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 2.16 r_work: 0.3715 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8890 Z= 0.147 Angle : 0.554 5.773 12231 Z= 0.285 Chirality : 0.042 0.142 1329 Planarity : 0.005 0.056 1421 Dihedral : 14.733 82.547 1377 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.16 % Allowed : 10.94 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.28), residues: 951 helix: 1.13 (0.30), residues: 323 sheet: -0.29 (0.40), residues: 166 loop : -1.00 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 356 TYR 0.015 0.001 TYR B 144 PHE 0.009 0.001 PHE B 130 TRP 0.019 0.001 TRP A 402 HIS 0.005 0.001 HIS B 361 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 8890) covalent geometry : angle 0.55448 (12231) hydrogen bonds : bond 0.03664 ( 312) hydrogen bonds : angle 4.23696 ( 831) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 0.295 Fit side-chains REVERT: A 516 GLU cc_start: 0.6539 (tp30) cc_final: 0.5537 (pm20) outliers start: 10 outliers final: 8 residues processed: 112 average time/residue: 0.0811 time to fit residues: 12.6341 Evaluate side-chains 104 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 423 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 3 optimal weight: 30.0000 chunk 17 optimal weight: 9.9990 chunk 96 optimal weight: 20.0000 chunk 48 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 367 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.210633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.173951 restraints weight = 9777.505| |-----------------------------------------------------------------------------| r_work (start): 0.4002 rms_B_bonded: 2.08 r_work: 0.3732 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8890 Z= 0.200 Angle : 0.610 6.387 12231 Z= 0.315 Chirality : 0.044 0.153 1329 Planarity : 0.006 0.056 1421 Dihedral : 15.000 84.140 1377 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 1.51 % Allowed : 13.39 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.28), residues: 951 helix: 0.91 (0.30), residues: 322 sheet: -0.78 (0.39), residues: 176 loop : -1.07 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 358 TYR 0.021 0.002 TYR B 144 PHE 0.011 0.002 PHE B 130 TRP 0.019 0.002 TRP A 402 HIS 0.006 0.001 HIS B 361 Details of bonding type rmsd covalent geometry : bond 0.00480 ( 8890) covalent geometry : angle 0.61034 (12231) hydrogen bonds : bond 0.04126 ( 312) hydrogen bonds : angle 4.41887 ( 831) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.301 Fit side-chains REVERT: A 516 GLU cc_start: 0.6600 (tp30) cc_final: 0.5591 (pm20) outliers start: 13 outliers final: 11 residues processed: 114 average time/residue: 0.0832 time to fit residues: 13.2989 Evaluate side-chains 106 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 423 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 chunk 72 optimal weight: 6.9990 chunk 96 optimal weight: 20.0000 chunk 30 optimal weight: 6.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 GLN B 367 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.212562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.174039 restraints weight = 9667.893| |-----------------------------------------------------------------------------| r_work (start): 0.4024 rms_B_bonded: 2.06 r_work: 0.3778 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 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 : 0.003 0.038 8890 Z= 0.142 Angle : 0.554 6.068 12231 Z= 0.286 Chirality : 0.041 0.144 1329 Planarity : 0.005 0.054 1421 Dihedral : 14.834 82.978 1377 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 1.05 % Allowed : 14.90 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.28), residues: 951 helix: 1.13 (0.30), residues: 322 sheet: -0.75 (0.39), residues: 176 loop : -1.02 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 358 TYR 0.014 0.001 TYR B 144 PHE 0.008 0.001 PHE B 130 TRP 0.019 0.001 TRP A 402 HIS 0.004 0.001 HIS B 208 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 8890) covalent geometry : angle 0.55401 (12231) hydrogen bonds : bond 0.03524 ( 312) hydrogen bonds : angle 4.23033 ( 831) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.287 Fit side-chains REVERT: A 516 GLU cc_start: 0.6604 (tp30) cc_final: 0.5658 (pm20) REVERT: B 181 TYR cc_start: 0.7699 (t80) cc_final: 0.7375 (t80) outliers start: 9 outliers final: 9 residues processed: 111 average time/residue: 0.0945 time to fit residues: 14.4477 Evaluate side-chains 106 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 423 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 73 optimal weight: 1.9990 chunk 62 optimal weight: 20.0000 chunk 63 optimal weight: 0.0000 chunk 27 optimal weight: 9.9990 chunk 38 optimal weight: 0.7980 chunk 35 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 57 optimal weight: 9.9990 chunk 87 optimal weight: 6.9990 chunk 68 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 overall best weight: 1.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 GLN B 367 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.214888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.177199 restraints weight = 9602.511| |-----------------------------------------------------------------------------| r_work (start): 0.4056 rms_B_bonded: 2.08 r_work: 0.3804 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8890 Z= 0.117 Angle : 0.537 6.037 12231 Z= 0.276 Chirality : 0.040 0.140 1329 Planarity : 0.005 0.052 1421 Dihedral : 14.705 81.965 1377 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.86 % Allowed : 15.60 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.28), residues: 951 helix: 1.32 (0.31), residues: 322 sheet: -0.72 (0.39), residues: 178 loop : -0.98 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 83 TYR 0.019 0.001 TYR A 319 PHE 0.008 0.001 PHE A 77 TRP 0.018 0.001 TRP A 402 HIS 0.005 0.001 HIS B 208 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 8890) covalent geometry : angle 0.53653 (12231) hydrogen bonds : bond 0.03274 ( 312) hydrogen bonds : angle 4.10650 ( 831) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.214 Fit side-chains REVERT: A 78 ARG cc_start: 0.6759 (mpt180) cc_final: 0.5443 (mtt180) REVERT: A 514 GLU cc_start: 0.7104 (mt-10) cc_final: 0.6429 (pt0) REVERT: A 516 GLU cc_start: 0.6550 (tp30) cc_final: 0.5653 (pm20) REVERT: B 181 TYR cc_start: 0.7606 (t80) cc_final: 0.7309 (t80) outliers start: 16 outliers final: 13 residues processed: 119 average time/residue: 0.0896 time to fit residues: 14.8742 Evaluate side-chains 111 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 423 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 27 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 chunk 90 optimal weight: 9.9990 chunk 70 optimal weight: 8.9990 chunk 96 optimal weight: 20.0000 chunk 67 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 28 optimal weight: 0.3980 chunk 87 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 80 optimal weight: 30.0000 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 GLN B 367 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.209880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.171930 restraints weight = 9808.573| |-----------------------------------------------------------------------------| r_work (start): 0.4047 rms_B_bonded: 2.15 r_work: 0.3789 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8890 Z= 0.118 Angle : 0.529 6.155 12231 Z= 0.272 Chirality : 0.040 0.140 1329 Planarity : 0.005 0.051 1421 Dihedral : 14.559 80.743 1377 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.86 % Allowed : 15.83 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.28), residues: 951 helix: 1.42 (0.31), residues: 322 sheet: -0.72 (0.39), residues: 180 loop : -0.93 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 358 TYR 0.017 0.001 TYR A 319 PHE 0.009 0.001 PHE A 227 TRP 0.017 0.001 TRP A 402 HIS 0.005 0.001 HIS B 208 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 8890) covalent geometry : angle 0.52943 (12231) hydrogen bonds : bond 0.03182 ( 312) hydrogen bonds : angle 4.01096 ( 831) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 0.276 Fit side-chains REVERT: A 78 ARG cc_start: 0.6715 (mpt180) cc_final: 0.5451 (mtt180) REVERT: A 514 GLU cc_start: 0.7076 (mt-10) cc_final: 0.6384 (pt0) REVERT: A 516 GLU cc_start: 0.6404 (tp30) cc_final: 0.5562 (pm20) REVERT: B 181 TYR cc_start: 0.7592 (t80) cc_final: 0.7302 (t80) outliers start: 16 outliers final: 13 residues processed: 116 average time/residue: 0.0882 time to fit residues: 14.3565 Evaluate side-chains 112 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 423 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 54 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 chunk 85 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 chunk 16 optimal weight: 0.3980 chunk 73 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 51 optimal weight: 9.9990 chunk 69 optimal weight: 4.9990 chunk 72 optimal weight: 6.9990 overall best weight: 4.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 GLN B 367 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.207211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.168605 restraints weight = 9700.967| |-----------------------------------------------------------------------------| r_work (start): 0.4008 rms_B_bonded: 2.31 r_work: 0.3731 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8890 Z= 0.170 Angle : 0.577 6.408 12231 Z= 0.298 Chirality : 0.042 0.146 1329 Planarity : 0.005 0.051 1421 Dihedral : 14.654 81.854 1377 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 1.51 % Allowed : 17.23 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.28), residues: 951 helix: 1.21 (0.30), residues: 322 sheet: -0.72 (0.39), residues: 176 loop : -1.03 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 358 TYR 0.018 0.002 TYR B 144 PHE 0.013 0.001 PHE A 227 TRP 0.016 0.002 TRP A 402 HIS 0.004 0.001 HIS B 361 Details of bonding type rmsd covalent geometry : bond 0.00413 ( 8890) covalent geometry : angle 0.57696 (12231) hydrogen bonds : bond 0.03637 ( 312) hydrogen bonds : angle 4.17496 ( 831) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.314 Fit side-chains REVERT: A 78 ARG cc_start: 0.6718 (mpt180) cc_final: 0.5428 (mtt180) REVERT: A 514 GLU cc_start: 0.7182 (mt-10) cc_final: 0.6378 (pt0) REVERT: A 516 GLU cc_start: 0.6579 (tp30) cc_final: 0.5630 (pm20) REVERT: B 181 TYR cc_start: 0.7709 (t80) cc_final: 0.7379 (t80) outliers start: 13 outliers final: 12 residues processed: 111 average time/residue: 0.0859 time to fit residues: 13.2799 Evaluate side-chains 105 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 423 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 97 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 2 optimal weight: 30.0000 chunk 6 optimal weight: 0.1980 chunk 13 optimal weight: 20.0000 chunk 21 optimal weight: 8.9990 chunk 36 optimal weight: 0.4980 chunk 41 optimal weight: 8.9990 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 20.0000 overall best weight: 3.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 GLN B 367 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.207253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.168694 restraints weight = 9698.383| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 2.13 r_work: 0.3739 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8890 Z= 0.160 Angle : 0.574 6.438 12231 Z= 0.296 Chirality : 0.042 0.145 1329 Planarity : 0.005 0.051 1421 Dihedral : 14.643 81.851 1377 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 1.75 % Allowed : 17.11 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.28), residues: 951 helix: 1.19 (0.30), residues: 322 sheet: -0.76 (0.39), residues: 176 loop : -1.05 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 356 TYR 0.024 0.002 TYR A 319 PHE 0.013 0.001 PHE A 227 TRP 0.016 0.001 TRP A 402 HIS 0.004 0.001 HIS B 208 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 8890) covalent geometry : angle 0.57428 (12231) hydrogen bonds : bond 0.03575 ( 312) hydrogen bonds : angle 4.17705 ( 831) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.271 Fit side-chains REVERT: A 78 ARG cc_start: 0.6728 (mpt180) cc_final: 0.5458 (mtt180) REVERT: A 303 LEU cc_start: 0.7068 (OUTLIER) cc_final: 0.6795 (mt) REVERT: A 514 GLU cc_start: 0.7157 (mt-10) cc_final: 0.6372 (pt0) REVERT: A 516 GLU cc_start: 0.6585 (tp30) cc_final: 0.5639 (pm20) REVERT: B 181 TYR cc_start: 0.7687 (t80) cc_final: 0.7364 (t80) outliers start: 15 outliers final: 14 residues processed: 108 average time/residue: 0.0913 time to fit residues: 13.7652 Evaluate side-chains 107 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 423 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 69 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 48 optimal weight: 8.9990 chunk 64 optimal weight: 8.9990 chunk 96 optimal weight: 20.0000 chunk 19 optimal weight: 6.9990 chunk 17 optimal weight: 0.6980 chunk 28 optimal weight: 20.0000 chunk 74 optimal weight: 8.9990 chunk 90 optimal weight: 6.9990 overall best weight: 4.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 GLN B 367 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.207223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.168775 restraints weight = 9724.885| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 2.25 r_work: 0.3667 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8890 Z= 0.160 Angle : 0.574 6.438 12231 Z= 0.296 Chirality : 0.042 0.145 1329 Planarity : 0.005 0.051 1421 Dihedral : 14.643 81.851 1377 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 1.75 % Allowed : 17.35 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.28), residues: 951 helix: 1.19 (0.30), residues: 322 sheet: -0.76 (0.39), residues: 176 loop : -1.05 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 356 TYR 0.024 0.002 TYR A 319 PHE 0.013 0.001 PHE A 227 TRP 0.016 0.001 TRP A 402 HIS 0.004 0.001 HIS B 208 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 8890) covalent geometry : angle 0.57427 (12231) hydrogen bonds : bond 0.03575 ( 312) hydrogen bonds : angle 4.17705 ( 831) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1902 Ramachandran restraints generated. 951 Oldfield, 0 Emsley, 951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.348 Fit side-chains REVERT: A 78 ARG cc_start: 0.6712 (mpt180) cc_final: 0.5429 (mtt180) REVERT: A 303 LEU cc_start: 0.7059 (OUTLIER) cc_final: 0.6776 (mt) REVERT: A 514 GLU cc_start: 0.7218 (mt-10) cc_final: 0.6386 (pt0) REVERT: A 516 GLU cc_start: 0.6599 (tp30) cc_final: 0.5639 (pm20) REVERT: B 181 TYR cc_start: 0.7713 (t80) cc_final: 0.7373 (t80) outliers start: 15 outliers final: 14 residues processed: 104 average time/residue: 0.0874 time to fit residues: 12.7956 Evaluate side-chains 107 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 422 LEU Chi-restraints excluded: chain B residue 423 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 12 optimal weight: 20.0000 chunk 44 optimal weight: 40.0000 chunk 36 optimal weight: 0.9980 chunk 65 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 84 optimal weight: 10.0000 chunk 16 optimal weight: 20.0000 chunk 91 optimal weight: 5.9990 chunk 79 optimal weight: 9.9990 chunk 22 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 GLN B 367 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.207223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.168765 restraints weight = 9717.179| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 2.25 r_work: 0.3674 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8890 Z= 0.160 Angle : 0.574 6.438 12231 Z= 0.296 Chirality : 0.042 0.145 1329 Planarity : 0.005 0.051 1421 Dihedral : 14.643 81.851 1377 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 1.75 % Allowed : 17.35 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.28), residues: 951 helix: 1.19 (0.30), residues: 322 sheet: -0.76 (0.39), residues: 176 loop : -1.05 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 356 TYR 0.024 0.002 TYR A 319 PHE 0.013 0.001 PHE A 227 TRP 0.016 0.001 TRP A 402 HIS 0.004 0.001 HIS B 208 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 8890) covalent geometry : angle 0.57427 (12231) hydrogen bonds : bond 0.03575 ( 312) hydrogen bonds : angle 4.17705 ( 831) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1738.83 seconds wall clock time: 30 minutes 34.31 seconds (1834.31 seconds total)