Starting phenix.real_space_refine on Sat Jul 26 08:59:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z2d_14462/07_2025/7z2d_14462.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z2d_14462/07_2025/7z2d_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_14462/07_2025/7z2d_14462.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z2d_14462/07_2025/7z2d_14462.map" model { file = "/net/cci-nas-00/data/ceres_data/7z2d_14462/07_2025/7z2d_14462.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z2d_14462/07_2025/7z2d_14462.cif" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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:plan2': 1, ' DA%5*END:plan': 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: 5.29, per 1000 atoms: 0.62 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: 2.66 Conformation dependent library (CDL) restraints added in 884.1 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: 2.94 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: 2.43 Time building geometry restraints manager: 2.80 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: 0.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.220 Find NCS groups from input model: 0.080 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: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.760 ------------------------------------------------------------------------------- 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 : 7.33 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.019 0.001 TRP A 402 HIS 0.006 0.001 HIS B 208 PHE 0.010 0.001 PHE B 130 TYR 0.013 0.001 TYR A 319 ARG 0.002 0.000 ARG A 83 Details of bonding type rmsd hydrogen bonds : bond 0.13935 ( 312) hydrogen bonds : angle 5.84384 ( 831) covalent geometry : bond 0.00444 ( 8890) covalent geometry : angle 0.66176 (12231) *********************** 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 : 0.860 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.2028 time to fit residues: 33.8184 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 : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 20.0000 chunk 74 optimal weight: 6.9990 chunk 41 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 50 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 chunk 29 optimal weight: 20.0000 chunk 46 optimal weight: 30.0000 chunk 57 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- 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 = 0.4342 r_free = 0.4342 target = 0.207526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.169302 restraints weight = 9620.521| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 2.08 r_work: 0.3727 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 8890 Z= 0.280 Angle : 0.701 7.162 12231 Z= 0.365 Chirality : 0.047 0.162 1329 Planarity : 0.006 0.064 1421 Dihedral : 14.938 86.651 1377 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 1.28 % Allowed : 9.20 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.27), residues: 951 helix: 0.58 (0.30), residues: 325 sheet: -0.68 (0.40), residues: 166 loop : -1.29 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 402 HIS 0.006 0.001 HIS B 361 PHE 0.016 0.002 PHE B 130 TYR 0.024 0.002 TYR B 144 ARG 0.004 0.001 ARG A 358 Details of bonding type rmsd hydrogen bonds : bond 0.04979 ( 312) hydrogen bonds : angle 4.72472 ( 831) covalent geometry : bond 0.00675 ( 8890) covalent geometry : angle 0.70093 (12231) *********************** 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: 11 poor density : 103 time to evaluate : 1.002 Fit side-chains REVERT: A 516 GLU cc_start: 0.6734 (tp30) cc_final: 0.5527 (pm20) outliers start: 11 outliers final: 6 residues processed: 110 average time/residue: 0.2256 time to fit residues: 33.9713 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 : 0.896 ------------------------------------------------------------------------------- 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 73 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 46 optimal weight: 30.0000 chunk 94 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 20 optimal weight: 20.0000 chunk 22 optimal weight: 0.6980 chunk 35 optimal weight: 5.9990 chunk 76 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 ASN A 500 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 = 0.4429 r_free = 0.4429 target = 0.216769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.179038 restraints weight = 9591.650| |-----------------------------------------------------------------------------| r_work (start): 0.4049 rms_B_bonded: 1.87 r_work: 0.3811 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8890 Z= 0.105 Angle : 0.523 5.606 12231 Z= 0.269 Chirality : 0.040 0.141 1329 Planarity : 0.005 0.057 1421 Dihedral : 14.569 81.638 1377 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.35 % Allowed : 12.22 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.28), residues: 951 helix: 1.21 (0.30), residues: 326 sheet: -0.36 (0.39), residues: 169 loop : -0.99 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 402 HIS 0.005 0.001 HIS B 208 PHE 0.007 0.001 PHE A 346 TYR 0.014 0.001 TYR A 144 ARG 0.002 0.000 ARG A 83 Details of bonding type rmsd hydrogen bonds : bond 0.03203 ( 312) hydrogen bonds : angle 4.10729 ( 831) covalent geometry : bond 0.00243 ( 8890) covalent geometry : angle 0.52325 (12231) *********************** 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 113 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 110 time to evaluate : 0.943 Fit side-chains REVERT: A 516 GLU cc_start: 0.6419 (tp30) cc_final: 0.5521 (pm20) outliers start: 3 outliers final: 3 residues processed: 113 average time/residue: 0.2238 time to fit residues: 34.7501 Evaluate side-chains 95 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 92 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 47 ILE 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 9 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 chunk 81 optimal weight: 20.0000 chunk 75 optimal weight: 8.9990 chunk 73 optimal weight: 30.0000 chunk 16 optimal weight: 0.3980 chunk 40 optimal weight: 7.9990 chunk 97 optimal weight: 20.0000 chunk 68 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 92 optimal weight: 10.0000 overall best weight: 6.4788 ------------------------------------------------------------------------------- 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 = 0.4366 r_free = 0.4366 target = 0.210069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.173192 restraints weight = 9661.913| |-----------------------------------------------------------------------------| r_work (start): 0.3995 rms_B_bonded: 2.09 r_work: 0.3726 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8890 Z= 0.229 Angle : 0.645 6.256 12231 Z= 0.334 Chirality : 0.045 0.157 1329 Planarity : 0.006 0.056 1421 Dihedral : 15.005 84.699 1377 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 1.28 % Allowed : 13.74 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.28), residues: 951 helix: 0.85 (0.30), residues: 322 sheet: -0.85 (0.38), residues: 176 loop : -1.12 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 402 HIS 0.006 0.001 HIS B 361 PHE 0.012 0.002 PHE B 130 TYR 0.022 0.002 TYR B 144 ARG 0.003 0.000 ARG A 358 Details of bonding type rmsd hydrogen bonds : bond 0.04337 ( 312) hydrogen bonds : angle 4.52168 ( 831) covalent geometry : bond 0.00549 ( 8890) covalent geometry : angle 0.64517 (12231) *********************** 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 112 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.930 Fit side-chains REVERT: A 516 GLU cc_start: 0.6713 (tp30) cc_final: 0.5680 (pm20) outliers start: 11 outliers final: 10 residues processed: 109 average time/residue: 0.2349 time to fit residues: 35.2246 Evaluate side-chains 105 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 1.160 ------------------------------------------------------------------------------- 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 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 64 optimal weight: 20.0000 chunk 14 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 30 optimal weight: 10.0000 chunk 96 optimal weight: 20.0000 chunk 74 optimal weight: 9.9990 chunk 84 optimal weight: 20.0000 chunk 11 optimal weight: 5.9990 chunk 28 optimal weight: 20.0000 chunk 54 optimal weight: 8.9990 chunk 63 optimal weight: 0.0670 overall best weight: 4.6126 ------------------------------------------------------------------------------- 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 = 0.4385 r_free = 0.4385 target = 0.212110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.175839 restraints weight = 9629.216| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 2.10 r_work: 0.3752 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8890 Z= 0.174 Angle : 0.590 6.412 12231 Z= 0.305 Chirality : 0.043 0.148 1329 Planarity : 0.005 0.055 1421 Dihedral : 14.887 84.165 1377 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 1.51 % Allowed : 15.95 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.28), residues: 951 helix: 0.95 (0.30), residues: 322 sheet: -0.84 (0.39), residues: 176 loop : -1.14 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 402 HIS 0.004 0.001 HIS B 361 PHE 0.011 0.001 PHE B 130 TYR 0.018 0.002 TYR B 144 ARG 0.002 0.000 ARG A 358 Details of bonding type rmsd hydrogen bonds : bond 0.03855 ( 312) hydrogen bonds : angle 4.38185 ( 831) covalent geometry : bond 0.00418 ( 8890) covalent geometry : angle 0.58978 (12231) *********************** 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: 13 poor density : 100 time to evaluate : 0.950 Fit side-chains REVERT: A 516 GLU cc_start: 0.6685 (tp30) cc_final: 0.5666 (pm20) outliers start: 13 outliers final: 13 residues processed: 111 average time/residue: 0.2148 time to fit residues: 33.0361 Evaluate side-chains 106 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.910 ------------------------------------------------------------------------------- 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 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 423 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 61 optimal weight: 6.9990 chunk 17 optimal weight: 7.9990 chunk 49 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 4 optimal weight: 10.0000 chunk 37 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 75 optimal weight: 8.9990 chunk 88 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 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 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 = 0.4362 r_free = 0.4362 target = 0.209802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.172714 restraints weight = 9633.927| |-----------------------------------------------------------------------------| r_work (start): 0.4015 rms_B_bonded: 2.09 r_work: 0.3746 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.1777 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= 0.202 Angle : 0.620 6.625 12231 Z= 0.321 Chirality : 0.044 0.153 1329 Planarity : 0.006 0.055 1421 Dihedral : 14.956 84.909 1377 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 2.44 % Allowed : 17.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.28), residues: 951 helix: 0.90 (0.30), residues: 315 sheet: -1.04 (0.38), residues: 178 loop : -1.13 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 402 HIS 0.005 0.001 HIS B 361 PHE 0.011 0.002 PHE A 61 TYR 0.023 0.002 TYR A 319 ARG 0.003 0.000 ARG A 358 Details of bonding type rmsd hydrogen bonds : bond 0.04101 ( 312) hydrogen bonds : angle 4.47046 ( 831) covalent geometry : bond 0.00487 ( 8890) covalent geometry : angle 0.61982 (12231) *********************** 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 121 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 1.005 Fit side-chains REVERT: A 516 GLU cc_start: 0.6685 (tp30) cc_final: 0.5667 (pm20) REVERT: B 181 TYR cc_start: 0.7751 (t80) cc_final: 0.7421 (t80) outliers start: 21 outliers final: 17 residues processed: 117 average time/residue: 0.2385 time to fit residues: 39.3293 Evaluate side-chains 110 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.943 ------------------------------------------------------------------------------- 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 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 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 74 LEU Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 381 VAL 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 65 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 62 optimal weight: 20.0000 chunk 35 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 53 optimal weight: 8.9990 chunk 86 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 chunk 44 optimal weight: 50.0000 chunk 95 optimal weight: 20.0000 overall best weight: 5.9988 ------------------------------------------------------------------------------- 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 = 0.4300 r_free = 0.4300 target = 0.204450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.165937 restraints weight = 9831.695| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 2.15 r_work: 0.3698 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8890 Z= 0.213 Angle : 0.631 6.887 12231 Z= 0.328 Chirality : 0.044 0.153 1329 Planarity : 0.006 0.056 1421 Dihedral : 14.962 85.600 1377 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 2.33 % Allowed : 18.04 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.28), residues: 951 helix: 0.81 (0.30), residues: 315 sheet: -1.05 (0.39), residues: 176 loop : -1.24 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 402 HIS 0.005 0.001 HIS B 361 PHE 0.015 0.002 PHE A 227 TYR 0.020 0.002 TYR B 144 ARG 0.003 0.000 ARG A 358 Details of bonding type rmsd hydrogen bonds : bond 0.04184 ( 312) hydrogen bonds : angle 4.52862 ( 831) covalent geometry : bond 0.00514 ( 8890) covalent geometry : angle 0.63077 (12231) *********************** 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 118 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.913 Fit side-chains REVERT: A 516 GLU cc_start: 0.6673 (tp30) cc_final: 0.5652 (pm20) REVERT: B 181 TYR cc_start: 0.7802 (t80) cc_final: 0.7453 (t80) outliers start: 20 outliers final: 18 residues processed: 115 average time/residue: 0.3747 time to fit residues: 59.3020 Evaluate side-chains 110 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 1.137 ------------------------------------------------------------------------------- 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 289 LEU Chi-restraints excluded: chain A residue 380 ILE 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 74 LEU Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 381 VAL 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 21 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 6 optimal weight: 30.0000 chunk 91 optimal weight: 4.9990 chunk 59 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 40.0000 chunk 84 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 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 182 GLN B 207 GLN B 242 GLN B 367 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.204427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.165521 restraints weight = 9899.427| |-----------------------------------------------------------------------------| r_work (start): 0.3974 rms_B_bonded: 2.15 r_work: 0.3716 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.1938 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= 0.202 Angle : 0.627 6.923 12231 Z= 0.326 Chirality : 0.044 0.152 1329 Planarity : 0.006 0.056 1421 Dihedral : 15.018 85.645 1377 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 2.68 % Allowed : 17.69 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.28), residues: 951 helix: 0.86 (0.30), residues: 317 sheet: -1.13 (0.38), residues: 178 loop : -1.28 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 402 HIS 0.005 0.001 HIS B 361 PHE 0.011 0.002 PHE A 227 TYR 0.020 0.002 TYR B 144 ARG 0.003 0.000 ARG A 358 Details of bonding type rmsd hydrogen bonds : bond 0.04071 ( 312) hydrogen bonds : angle 4.54057 ( 831) covalent geometry : bond 0.00490 ( 8890) covalent geometry : angle 0.62706 (12231) *********************** 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 118 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 95 time to evaluate : 3.167 Fit side-chains REVERT: A 516 GLU cc_start: 0.6657 (tp30) cc_final: 0.5633 (pm20) REVERT: B 181 TYR cc_start: 0.7795 (t80) cc_final: 0.7471 (t80) REVERT: B 410 TRP cc_start: 0.8092 (OUTLIER) cc_final: 0.7400 (p90) outliers start: 23 outliers final: 20 residues processed: 115 average time/residue: 0.3687 time to fit residues: 60.5195 Evaluate side-chains 112 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 1.017 ------------------------------------------------------------------------------- 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 289 LEU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 380 ILE 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 74 LEU Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 381 VAL Chi-restraints excluded: chain B residue 382 ILE Chi-restraints excluded: chain B residue 410 TRP 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 20 optimal weight: 0.6980 chunk 67 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 86 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 92 optimal weight: 10.0000 chunk 44 optimal weight: 50.0000 overall best weight: 4.1388 ------------------------------------------------------------------------------- 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 = 0.4321 r_free = 0.4321 target = 0.206332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.167672 restraints weight = 9718.586| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 2.16 r_work: 0.3715 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8890 Z= 0.165 Angle : 0.594 6.669 12231 Z= 0.307 Chirality : 0.042 0.146 1329 Planarity : 0.005 0.055 1421 Dihedral : 14.929 84.745 1377 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 2.10 % Allowed : 18.16 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.28), residues: 951 helix: 0.96 (0.30), residues: 322 sheet: -0.94 (0.39), residues: 176 loop : -1.27 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 402 HIS 0.004 0.001 HIS B 208 PHE 0.010 0.002 PHE A 227 TYR 0.017 0.002 TYR B 144 ARG 0.002 0.000 ARG A 358 Details of bonding type rmsd hydrogen bonds : bond 0.03726 ( 312) hydrogen bonds : angle 4.37821 ( 831) covalent geometry : bond 0.00399 ( 8890) covalent geometry : angle 0.59391 (12231) *********************** 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 114 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.921 Fit side-chains REVERT: A 516 GLU cc_start: 0.6603 (tp30) cc_final: 0.5619 (pm20) outliers start: 18 outliers final: 17 residues processed: 111 average time/residue: 0.2120 time to fit residues: 32.9520 Evaluate side-chains 106 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.970 ------------------------------------------------------------------------------- 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 369 THR Chi-restraints excluded: chain A residue 380 ILE 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 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 49 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 68 optimal weight: 0.6980 chunk 4 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 5 optimal weight: 8.9990 chunk 21 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 = 0.4348 r_free = 0.4348 target = 0.209490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.171203 restraints weight = 9639.754| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 2.19 r_work: 0.3756 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.1795 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= 0.117 Angle : 0.546 6.413 12231 Z= 0.281 Chirality : 0.041 0.143 1329 Planarity : 0.005 0.055 1421 Dihedral : 14.686 82.029 1377 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.16 % Allowed : 19.32 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.28), residues: 951 helix: 1.32 (0.31), residues: 319 sheet: -0.79 (0.39), residues: 177 loop : -1.15 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 402 HIS 0.004 0.001 HIS B 208 PHE 0.008 0.001 PHE B 77 TYR 0.015 0.001 TYR A 144 ARG 0.001 0.000 ARG A 125 Details of bonding type rmsd hydrogen bonds : bond 0.03189 ( 312) hydrogen bonds : angle 4.12612 ( 831) covalent geometry : bond 0.00281 ( 8890) covalent geometry : angle 0.54612 (12231) ********************** 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 117 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.872 Fit side-chains REVERT: A 516 GLU cc_start: 0.6454 (tp30) cc_final: 0.5617 (pm20) outliers start: 10 outliers final: 9 residues processed: 114 average time/residue: 0.2056 time to fit residues: 32.9354 Evaluate side-chains 110 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.872 ------------------------------------------------------------------------------- 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 493 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 74 LEU 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 46 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 97 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 38 optimal weight: 10.0000 chunk 93 optimal weight: 5.9990 chunk 92 optimal weight: 7.9990 chunk 43 optimal weight: 7.9990 chunk 17 optimal weight: 8.9990 chunk 87 optimal weight: 5.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 520 GLN 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 = 0.4320 r_free = 0.4320 target = 0.206394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.167814 restraints weight = 9728.326| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 2.15 r_work: 0.3732 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8890 Z= 0.175 Angle : 0.600 7.674 12231 Z= 0.310 Chirality : 0.043 0.146 1329 Planarity : 0.005 0.055 1421 Dihedral : 14.842 83.460 1377 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 1.40 % Allowed : 19.56 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.28), residues: 951 helix: 1.09 (0.30), residues: 322 sheet: -0.82 (0.39), residues: 176 loop : -1.21 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 402 HIS 0.004 0.001 HIS B 361 PHE 0.010 0.002 PHE A 227 TYR 0.018 0.002 TYR B 144 ARG 0.004 0.000 ARG B 356 Details of bonding type rmsd hydrogen bonds : bond 0.03789 ( 312) hydrogen bonds : angle 4.31062 ( 831) covalent geometry : bond 0.00424 ( 8890) covalent geometry : angle 0.59966 (12231) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4357.55 seconds wall clock time: 79 minutes 6.16 seconds (4746.16 seconds total)