Starting phenix.real_space_refine on Thu Jul 2 11:17:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7z2d_14462/07_2026/7z2d_14462.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z2d_14462/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/7z2d_14462/07_2026/7z2d_14462.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z2d_14462/07_2026/7z2d_14462.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7z2d_14462/07_2026/7z2d_14462.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z2d_14462/07_2026/7z2d_14462.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7z2d_14462/07_2026/7z2d_14462.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7z2d_14462/07_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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: 1.70, per 1000 atoms: 0.20 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: 0.60 Conformation dependent library (CDL) restraints added in 459.4 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: 0.89 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: 1.17 Time building geometry restraints manager: 0.87 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: 12125 2.98 - 5.95: 97 5.95 - 8.93: 7 8.93 - 11.91: 1 11.91 - 14.88: 1 Bond angle restraints: 12231 Sorted by residual: 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=" N3 DT E 0 " pdb=" C4 DT E 0 " pdb=" O4 DT E 0 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT E 18 " pdb=" C4 DT E 18 " pdb=" O4 DT E 18 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.69e+01 angle pdb=" N3 DT E -1 " pdb=" C4 DT E -1 " pdb=" O4 DT E -1 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.69e+01 angle pdb=" N3 DT E 17 " pdb=" C4 DT E 17 " pdb=" O4 DT E 17 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 ... (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: 36 71.36 - 89.20: 9 Dihedral angle restraints: 5207 sinusoidal: 2409 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 5204 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1176 0.076 - 0.152: 148 0.152 - 0.229: 3 0.229 - 0.305: 1 0.305 - 0.381: 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 -0.38 2.00e-01 2.50e+01 3.63e+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 -2.73 -2.47 -0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" C3' DA E 26 " pdb=" C4' DA E 26 " pdb=" O3' DA E 26 " pdb=" C2' DA E 26 " both_signs ideal model delta sigma weight residual False -2.73 -2.53 -0.20 2.00e-01 2.50e+01 1.04e+00 ... (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: 0.160 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.320 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 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= 0.243 Angle : 0.663 14.883 12231 Z= 0.372 Chirality : 0.046 0.381 1329 Planarity : 0.005 0.070 1421 Dihedral : 16.324 89.196 3403 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/Z covalent geometry : bond 0.00444 / 0.24 ( 8890) covalent geometry : angle 0.66254 / 0.37 (12231) hydrogen bonds : bond 0.13935 / 8.57 ( 312) hydrogen bonds : angle 5.84384 / 4.14 ( 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 : 0.271 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.0781 time to fit residues: 13.1474 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 : 0.268 ------------------------------------------------------------------------------- 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: 40.0000 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... ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 ASN A 332 GLN B 54 ASN B 182 GLN B 207 GLN B 367 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.218769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.183632 restraints weight = 9591.709| |-----------------------------------------------------------------------------| r_work (start): 0.4113 rms_B_bonded: 1.83 r_work: 0.3849 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.0836 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= 0.182 Angle : 0.609 6.521 12231 Z= 0.321 Chirality : 0.045 0.173 1329 Planarity : 0.005 0.062 1421 Dihedral : 14.482 82.355 1376 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 1.05 % Allowed : 6.52 % Favored : 92.43 % 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: -0.29 (0.28), residues: 951 helix: 1.04 (0.30), residues: 320 sheet: -0.41 (0.39), residues: 170 loop : -0.96 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 83 TYR 0.017 0.002 TYR B 144 PHE 0.013 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/Z covalent geometry : bond 0.00420 / 0.18 ( 8890) covalent geometry : angle 0.60899 / 0.32 (12231) hydrogen bonds : bond 0.04536 / 2.85 ( 312) hydrogen bonds : angle 4.36043 / 3.04 ( 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 114 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 0.205 Fit side-chains REVERT: A 516 GLU cc_start: 0.6604 (tp30) cc_final: 0.5470 (pm20) outliers start: 9 outliers final: 6 residues processed: 111 average time/residue: 0.0800 time to fit residues: 12.4922 Evaluate side-chains 101 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 95 time to evaluate : 0.292 ------------------------------------------------------------------------------- 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: 9.9990 chunk 42 optimal weight: 0.6980 chunk 73 optimal weight: 9.9990 chunk 6 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 64 optimal weight: 20.0000 chunk 66 optimal weight: 4.9990 chunk 32 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 255 ASN A 334 GLN B 367 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.217877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.180964 restraints weight = 9574.461| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 1.69 r_work: 0.3767 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3627 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.1067 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= 0.152 Angle : 0.565 5.673 12231 Z= 0.300 Chirality : 0.043 0.142 1329 Planarity : 0.005 0.056 1421 Dihedral : 14.632 82.518 1376 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 1.75 % Allowed : 9.31 % Favored : 88.94 % 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: -0.29 (0.28), residues: 951 helix: 1.02 (0.30), residues: 323 sheet: -0.45 (0.39), residues: 170 loop : -0.94 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 356 TYR 0.016 0.001 TYR B 144 PHE 0.009 0.001 PHE B 130 TRP 0.018 0.001 TRP A 402 HIS 0.004 0.001 HIS B 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 ( 8890) covalent geometry : angle 0.56548 / 0.30 (12231) hydrogen bonds : bond 0.04026 / 2.54 ( 312) hydrogen bonds : angle 4.28056 / 2.99 ( 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 117 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.220 Fit side-chains REVERT: A 47 ILE cc_start: 0.7561 (mm) cc_final: 0.7352 (mm) REVERT: A 516 GLU cc_start: 0.6576 (tp30) cc_final: 0.5482 (pm20) outliers start: 15 outliers final: 10 residues processed: 110 average time/residue: 0.0788 time to fit residues: 12.0530 Evaluate side-chains 107 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.290 ------------------------------------------------------------------------------- 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 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 309 ILE Chi-restraints excluded: chain B residue 422 LEU 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: 0.3980 chunk 89 optimal weight: 2.9990 chunk 3 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 chunk 96 optimal weight: 50.0000 chunk 48 optimal weight: 8.9990 chunk 36 optimal weight: 9.9990 chunk 53 optimal weight: 20.0000 chunk 25 optimal weight: 9.9990 chunk 65 optimal weight: 9.9990 overall best weight: 6.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.210301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.173260 restraints weight = 9766.057| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 2.03 r_work: 0.3690 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8890 Z= 0.225 Angle : 0.655 6.865 12231 Z= 0.347 Chirality : 0.046 0.162 1329 Planarity : 0.006 0.057 1421 Dihedral : 15.048 83.691 1376 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 1.63 % Allowed : 12.81 % Favored : 85.56 % 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: -0.75 (0.28), residues: 951 helix: 0.69 (0.30), residues: 324 sheet: -1.01 (0.38), residues: 178 loop : -1.10 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 358 TYR 0.023 0.002 TYR B 144 PHE 0.015 0.002 PHE B 130 TRP 0.020 0.002 TRP A 402 HIS 0.007 0.001 HIS B 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.23 ( 8890) covalent geometry : angle 0.65542 / 0.35 (12231) hydrogen bonds : bond 0.04625 / 3.01 ( 312) hydrogen bonds : angle 4.55671 / 3.21 ( 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 118 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.236 Fit side-chains REVERT: A 47 ILE cc_start: 0.7622 (mm) cc_final: 0.7178 (mt) REVERT: A 516 GLU cc_start: 0.6715 (tp30) cc_final: 0.5667 (pm20) outliers start: 14 outliers final: 11 residues processed: 113 average time/residue: 0.0832 time to fit residues: 13.0082 Evaluate side-chains 108 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 240 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 35 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 422 LEU 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: 20.0000 chunk 45 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 12 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 72 optimal weight: 9.9990 chunk 96 optimal weight: 50.0000 chunk 30 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 255 ASN B 367 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.210866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.173997 restraints weight = 9767.734| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 2.09 r_work: 0.3724 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8890 Z= 0.200 Angle : 0.620 7.265 12231 Z= 0.326 Chirality : 0.045 0.154 1329 Planarity : 0.006 0.056 1421 Dihedral : 15.023 83.387 1376 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 1.63 % Allowed : 14.67 % Favored : 83.70 % 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: -0.74 (0.28), residues: 951 helix: 0.75 (0.30), residues: 322 sheet: -0.93 (0.38), residues: 176 loop : -1.18 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 358 TYR 0.019 0.002 TYR B 144 PHE 0.011 0.002 PHE B 130 TRP 0.021 0.002 TRP A 402 HIS 0.006 0.001 HIS B 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.20 ( 8890) covalent geometry : angle 0.61959 / 0.33 (12231) hydrogen bonds : bond 0.04238 / 2.74 ( 312) hydrogen bonds : angle 4.50571 / 3.17 ( 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 119 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.301 Fit side-chains REVERT: A 47 ILE cc_start: 0.7628 (mm) cc_final: 0.7196 (mt) REVERT: A 516 GLU cc_start: 0.6710 (tp30) cc_final: 0.5654 (pm20) outliers start: 14 outliers final: 12 residues processed: 115 average time/residue: 0.0787 time to fit residues: 12.7797 Evaluate side-chains 108 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.259 ------------------------------------------------------------------------------- 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 422 LEU 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: 3.9990 chunk 62 optimal weight: 20.0000 chunk 63 optimal weight: 0.0970 chunk 27 optimal weight: 9.9990 chunk 38 optimal weight: 0.0020 chunk 35 optimal weight: 9.9990 chunk 97 optimal weight: 50.0000 chunk 57 optimal weight: 10.0000 chunk 87 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 overall best weight: 2.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 500 GLN B 242 GLN B 367 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.213516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.175293 restraints weight = 9649.807| |-----------------------------------------------------------------------------| r_work (start): 0.4016 rms_B_bonded: 2.05 r_work: 0.3762 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8890 Z= 0.128 Angle : 0.555 6.971 12231 Z= 0.293 Chirality : 0.042 0.139 1329 Planarity : 0.005 0.053 1421 Dihedral : 14.803 81.687 1376 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.75 % Allowed : 15.95 % 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: -0.42 (0.28), residues: 951 helix: 1.11 (0.30), residues: 322 sheet: -0.84 (0.39), residues: 177 loop : -1.04 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 83 TYR 0.015 0.001 TYR A 144 PHE 0.009 0.001 PHE A 77 TRP 0.020 0.001 TRP A 402 HIS 0.005 0.001 HIS B 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 8890) covalent geometry : angle 0.55479 / 0.29 (12231) hydrogen bonds : bond 0.03532 / 2.25 ( 312) hydrogen bonds : angle 4.23065 / 2.96 ( 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 119 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.192 Fit side-chains REVERT: A 47 ILE cc_start: 0.7562 (mm) cc_final: 0.7102 (mt) REVERT: A 516 GLU cc_start: 0.6613 (tp30) cc_final: 0.5644 (pm20) REVERT: B 181 TYR cc_start: 0.7678 (t80) cc_final: 0.7368 (t80) outliers start: 15 outliers final: 11 residues processed: 114 average time/residue: 0.0791 time to fit residues: 12.5624 Evaluate side-chains 110 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.240 ------------------------------------------------------------------------------- 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 B residue 47 ILE Chi-restraints excluded: chain B residue 54 ASN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 27 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 70 optimal weight: 6.9990 chunk 96 optimal weight: 50.0000 chunk 67 optimal weight: 0.0980 chunk 60 optimal weight: 0.9990 chunk 28 optimal weight: 20.0000 chunk 87 optimal weight: 0.0000 chunk 73 optimal weight: 5.9990 chunk 80 optimal weight: 7.9990 overall best weight: 2.0190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4403 r_free = 0.4403 target = 0.214119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.176697 restraints weight = 9730.105| |-----------------------------------------------------------------------------| r_work (start): 0.4057 rms_B_bonded: 2.14 r_work: 0.3802 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8890 Z= 0.122 Angle : 0.546 7.450 12231 Z= 0.288 Chirality : 0.041 0.139 1329 Planarity : 0.005 0.052 1421 Dihedral : 14.667 80.481 1376 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.28 % Allowed : 17.23 % Favored : 81.49 % 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: -0.31 (0.28), residues: 951 helix: 1.30 (0.30), residues: 320 sheet: -0.83 (0.39), residues: 180 loop : -1.01 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 83 TYR 0.014 0.001 TYR A 144 PHE 0.009 0.001 PHE A 77 TRP 0.019 0.001 TRP A 402 HIS 0.005 0.001 HIS B 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 8890) covalent geometry : angle 0.54634 / 0.29 (12231) hydrogen bonds : bond 0.03373 / 2.15 ( 312) hydrogen bonds : angle 4.12962 / 2.88 ( 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 116 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 0.306 Fit side-chains REVERT: A 47 ILE cc_start: 0.7490 (mm) cc_final: 0.7028 (mt) REVERT: A 516 GLU cc_start: 0.6556 (tp30) cc_final: 0.5618 (pm20) REVERT: B 181 TYR cc_start: 0.7615 (t80) cc_final: 0.7321 (t80) outliers start: 11 outliers final: 11 residues processed: 112 average time/residue: 0.0783 time to fit residues: 12.1971 Evaluate side-chains 108 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.268 ------------------------------------------------------------------------------- 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 289 LEU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 54 ASN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 54 optimal weight: 9.9990 chunk 24 optimal weight: 8.9990 chunk 85 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 16 optimal weight: 8.9990 chunk 73 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 51 optimal weight: 9.9990 chunk 69 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4374 r_free = 0.4374 target = 0.210846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.172848 restraints weight = 9697.002| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 2.01 r_work: 0.3756 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 8890 Z= 0.206 Angle : 0.621 7.147 12231 Z= 0.327 Chirality : 0.045 0.154 1329 Planarity : 0.006 0.053 1421 Dihedral : 14.800 81.858 1376 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 1.51 % Allowed : 17.69 % Favored : 80.79 % 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: -0.57 (0.28), residues: 951 helix: 0.99 (0.30), residues: 322 sheet: -0.88 (0.39), residues: 176 loop : -1.15 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 358 TYR 0.020 0.002 TYR B 144 PHE 0.013 0.002 PHE A 227 TRP 0.016 0.002 TRP A 402 HIS 0.006 0.001 HIS B 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.21 ( 8890) covalent geometry : angle 0.62120 / 0.33 (12231) hydrogen bonds : bond 0.04133 / 2.70 ( 312) hydrogen bonds : angle 4.36138 / 3.06 ( 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 111 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.280 Fit side-chains REVERT: A 47 ILE cc_start: 0.7617 (mm) cc_final: 0.7175 (mt) REVERT: A 516 GLU cc_start: 0.6657 (tp30) cc_final: 0.5634 (pm20) outliers start: 13 outliers final: 12 residues processed: 109 average time/residue: 0.0823 time to fit residues: 12.5986 Evaluate side-chains 101 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 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 417 VAL Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 54 ASN 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: 50.0000 chunk 93 optimal weight: 8.9990 chunk 25 optimal weight: 7.9990 chunk 2 optimal weight: 30.0000 chunk 6 optimal weight: 9.9990 chunk 13 optimal weight: 20.0000 chunk 21 optimal weight: 8.9990 chunk 36 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 175 ASN B 207 GLN B 367 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.210740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.172807 restraints weight = 9696.884| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 2.02 r_work: 0.3745 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8890 Z= 0.203 Angle : 0.624 7.158 12231 Z= 0.329 Chirality : 0.045 0.153 1329 Planarity : 0.005 0.053 1421 Dihedral : 14.897 82.426 1376 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 1.75 % Allowed : 17.93 % Favored : 80.33 % 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: -0.71 (0.28), residues: 951 helix: 0.88 (0.30), residues: 322 sheet: -0.92 (0.39), residues: 176 loop : -1.25 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 358 TYR 0.024 0.002 TYR A 319 PHE 0.012 0.002 PHE A 227 TRP 0.018 0.002 TRP A 402 HIS 0.006 0.001 HIS B 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.20 ( 8890) covalent geometry : angle 0.62419 / 0.33 (12231) hydrogen bonds : bond 0.04106 / 2.67 ( 312) hydrogen bonds : angle 4.44076 / 3.12 ( 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 : 0.270 Fit side-chains REVERT: A 47 ILE cc_start: 0.7660 (mm) cc_final: 0.7234 (mt) REVERT: A 516 GLU cc_start: 0.6643 (tp30) cc_final: 0.5634 (pm20) REVERT: B 181 TYR cc_start: 0.7750 (t80) cc_final: 0.7446 (t80) outliers start: 15 outliers final: 14 residues processed: 109 average time/residue: 0.0886 time to fit residues: 13.4307 Evaluate side-chains 107 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.290 ------------------------------------------------------------------------------- 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 289 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 B residue 35 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 54 ASN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 69 optimal weight: 0.8980 chunk 77 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 48 optimal weight: 10.0000 chunk 64 optimal weight: 8.9990 chunk 96 optimal weight: 50.0000 chunk 19 optimal weight: 8.9990 chunk 17 optimal weight: 6.9990 chunk 28 optimal weight: 20.0000 chunk 74 optimal weight: 8.9990 chunk 90 optimal weight: 10.0000 overall best weight: 5.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 242 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 = 0.4366 r_free = 0.4366 target = 0.210175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.172345 restraints weight = 9718.474| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 2.02 r_work: 0.3681 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 8890 Z= 0.211 Angle : 0.639 7.199 12231 Z= 0.337 Chirality : 0.045 0.154 1329 Planarity : 0.006 0.053 1421 Dihedral : 14.975 82.886 1376 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 2.10 % Allowed : 17.69 % Favored : 80.21 % 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: -0.80 (0.28), residues: 951 helix: 0.83 (0.30), residues: 322 sheet: -1.02 (0.39), residues: 176 loop : -1.30 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 358 TYR 0.026 0.002 TYR A 319 PHE 0.013 0.002 PHE A 227 TRP 0.018 0.002 TRP A 402 HIS 0.005 0.001 HIS B 361 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.21 ( 8890) covalent geometry : angle 0.63861 / 0.34 (12231) hydrogen bonds : bond 0.04227 / 2.75 ( 312) hydrogen bonds : angle 4.51070 / 3.17 ( 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 113 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.230 Fit side-chains REVERT: A 47 ILE cc_start: 0.7665 (mm) cc_final: 0.7257 (mt) REVERT: A 516 GLU cc_start: 0.6579 (tp30) cc_final: 0.5518 (pm20) REVERT: B 181 TYR cc_start: 0.7735 (t80) cc_final: 0.7366 (t80) outliers start: 18 outliers final: 17 residues processed: 110 average time/residue: 0.0782 time to fit residues: 12.0345 Evaluate side-chains 111 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 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 289 LEU Chi-restraints excluded: chain A residue 323 LYS 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 10 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 54 ASN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 12 optimal weight: 0.0770 chunk 44 optimal weight: 40.0000 chunk 36 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 84 optimal weight: 8.9990 chunk 16 optimal weight: 6.9990 chunk 91 optimal weight: 0.8980 chunk 79 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 6 optimal weight: 20.0000 overall best weight: 2.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 367 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.213374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.177084 restraints weight = 9607.965| |-----------------------------------------------------------------------------| r_work (start): 0.4048 rms_B_bonded: 2.15 r_work: 0.3769 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8890 Z= 0.127 Angle : 0.569 6.767 12231 Z= 0.300 Chirality : 0.042 0.138 1329 Planarity : 0.005 0.052 1421 Dihedral : 14.845 80.943 1376 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.75 % Allowed : 17.81 % Favored : 80.44 % 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: -0.49 (0.28), residues: 951 helix: 1.16 (0.30), residues: 321 sheet: -0.91 (0.39), residues: 177 loop : -1.15 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 125 TYR 0.014 0.001 TYR A 144 PHE 0.008 0.001 PHE A 227 TRP 0.022 0.001 TRP A 402 HIS 0.005 0.001 HIS B 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 8890) covalent geometry : angle 0.56859 / 0.30 (12231) hydrogen bonds : bond 0.03475 / 2.23 ( 312) hydrogen bonds : angle 4.25691 / 2.97 ( 831) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1675.06 seconds wall clock time: 29 minutes 29.50 seconds (1769.50 seconds total)