Starting phenix.real_space_refine on Thu Feb 13 00:07:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z2d_14462/02_2025/7z2d_14462.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z2d_14462/02_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_14462/02_2025/7z2d_14462.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z2d_14462/02_2025/7z2d_14462.map" model { file = "/net/cci-nas-00/data/ceres_data/7z2d_14462/02_2025/7z2d_14462.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z2d_14462/02_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 5.39, per 1000 atoms: 0.63 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: 2.23 Conformation dependent library (CDL) restraints added in 855.7 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: 2.65 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: 2.38 Time building geometry restraints manager: 2.54 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: 0.070 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: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.770 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.340 ------------------------------------------------------------------------------- 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= 0.267 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 *********************** 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 : 0.937 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.2239 time to fit residues: 37.1885 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 : 0.900 ------------------------------------------------------------------------------- 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 = 0.169299 restraints weight = 9620.815| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 2.08 r_work: 0.3728 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 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= 0.430 Angle : 0.701 7.165 12231 Z= 0.365 Chirality : 0.047 0.162 1329 Planarity : 0.006 0.064 1421 Dihedral : 14.939 86.653 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 *********************** 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 : 0.882 Fit side-chains REVERT: A 516 GLU cc_start: 0.6735 (tp30) cc_final: 0.5529 (pm20) outliers start: 11 outliers final: 6 residues processed: 110 average time/residue: 0.2293 time to fit residues: 34.8193 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 : 1.005 ------------------------------------------------------------------------------- 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: 6.9990 chunk 39 optimal weight: 0.9980 chunk 87 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 46 optimal weight: 30.0000 chunk 94 optimal weight: 6.9990 chunk 26 optimal weight: 0.0060 chunk 20 optimal weight: 20.0000 chunk 22 optimal weight: 0.8980 chunk 35 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 overall best weight: 1.1198 ------------------------------------------------------------------------------- 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 = 0.4428 r_free = 0.4428 target = 0.216681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.179755 restraints weight = 9583.236| |-----------------------------------------------------------------------------| r_work (start): 0.4069 rms_B_bonded: 2.05 r_work: 0.3810 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8890 Z= 0.157 Angle : 0.523 5.620 12231 Z= 0.268 Chirality : 0.040 0.141 1329 Planarity : 0.005 0.057 1421 Dihedral : 14.598 81.303 1377 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.47 % Allowed : 11.99 % Favored : 87.54 % 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: -0.20 (0.28), residues: 951 helix: 1.20 (0.30), residues: 326 sheet: -0.37 (0.39), residues: 169 loop : -1.01 (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 0.009 0.001 PHE A 346 TYR 0.014 0.001 TYR A 144 ARG 0.002 0.000 ARG A 83 *********************** 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 115 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 111 time to evaluate : 0.908 Fit side-chains REVERT: A 516 GLU cc_start: 0.6412 (tp30) cc_final: 0.5506 (pm20) REVERT: B 181 TYR cc_start: 0.7699 (t80) cc_final: 0.7421 (t80) outliers start: 4 outliers final: 3 residues processed: 114 average time/residue: 0.2193 time to fit residues: 34.4071 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 : 0.974 ------------------------------------------------------------------------------- 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: 10.0000 chunk 14 optimal weight: 9.9990 chunk 81 optimal weight: 20.0000 chunk 75 optimal weight: 4.9990 chunk 73 optimal weight: 30.0000 chunk 16 optimal weight: 0.7980 chunk 40 optimal weight: 7.9990 chunk 97 optimal weight: 10.0000 chunk 68 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 overall best weight: 5.9588 ------------------------------------------------------------------------------- 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 = 0.4373 r_free = 0.4373 target = 0.210841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.173876 restraints weight = 9660.101| |-----------------------------------------------------------------------------| r_work (start): 0.4004 rms_B_bonded: 2.09 r_work: 0.3733 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.1545 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= 0.327 Angle : 0.624 6.176 12231 Z= 0.322 Chirality : 0.044 0.154 1329 Planarity : 0.006 0.056 1421 Dihedral : 14.886 83.906 1377 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 1.28 % Allowed : 13.85 % Favored : 84.87 % 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: -0.52 (0.28), residues: 951 helix: 0.97 (0.30), residues: 322 sheet: -0.81 (0.38), residues: 176 loop : -1.08 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 402 HIS 0.006 0.001 HIS B 361 PHE 0.012 0.002 PHE B 130 TYR 0.021 0.002 TYR B 144 ARG 0.003 0.000 ARG A 358 *********************** 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 114 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.949 Fit side-chains REVERT: A 516 GLU cc_start: 0.6591 (tp30) cc_final: 0.5552 (pm20) outliers start: 11 outliers final: 9 residues processed: 111 average time/residue: 0.2189 time to fit residues: 33.6857 Evaluate side-chains 102 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 0.894 ------------------------------------------------------------------------------- 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 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: 10.0000 chunk 15 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 96 optimal weight: 20.0000 chunk 74 optimal weight: 8.9990 chunk 84 optimal weight: 20.0000 chunk 11 optimal weight: 5.9990 chunk 28 optimal weight: 20.0000 chunk 54 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 overall best weight: 4.3788 ------------------------------------------------------------------------------- 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 = 0.4387 r_free = 0.4387 target = 0.212341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.176057 restraints weight = 9615.880| |-----------------------------------------------------------------------------| r_work (start): 0.4038 rms_B_bonded: 2.12 r_work: 0.3766 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8890 Z= 0.256 Angle : 0.578 6.372 12231 Z= 0.299 Chirality : 0.042 0.148 1329 Planarity : 0.005 0.055 1421 Dihedral : 14.792 83.587 1377 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 1.16 % Allowed : 16.18 % Favored : 82.65 % 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: -0.51 (0.28), residues: 951 helix: 1.03 (0.30), residues: 322 sheet: -0.85 (0.38), residues: 176 loop : -1.10 (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 208 PHE 0.010 0.002 PHE B 130 TYR 0.017 0.002 TYR B 144 ARG 0.002 0.000 ARG A 358 *********************** 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: 10 poor density : 103 time to evaluate : 0.893 Fit side-chains REVERT: A 514 GLU cc_start: 0.7191 (mt-10) cc_final: 0.6391 (pt0) REVERT: A 516 GLU cc_start: 0.6646 (tp30) cc_final: 0.5659 (pm20) REVERT: B 181 TYR cc_start: 0.7707 (t80) cc_final: 0.7392 (t80) outliers start: 10 outliers final: 10 residues processed: 111 average time/residue: 0.2151 time to fit residues: 33.1148 Evaluate side-chains 103 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.865 ------------------------------------------------------------------------------- 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 493 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 423 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 61 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 4 optimal weight: 10.0000 chunk 37 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 7 optimal weight: 20.0000 chunk 75 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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 = 0.4361 r_free = 0.4361 target = 0.209568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.172740 restraints weight = 9618.583| |-----------------------------------------------------------------------------| r_work (start): 0.4014 rms_B_bonded: 2.08 r_work: 0.3738 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8890 Z= 0.343 Angle : 0.643 6.856 12231 Z= 0.334 Chirality : 0.045 0.157 1329 Planarity : 0.006 0.055 1421 Dihedral : 15.032 85.409 1377 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 2.44 % Allowed : 16.76 % 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 (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: -0.77 (0.28), residues: 951 helix: 0.84 (0.30), residues: 317 sheet: -1.08 (0.38), residues: 178 loop : -1.21 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 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 0.004 0.000 ARG A 358 *********************** 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: 21 poor density : 98 time to evaluate : 0.975 Fit side-chains REVERT: A 47 ILE cc_start: 0.7661 (mm) cc_final: 0.7199 (mt) REVERT: A 514 GLU cc_start: 0.7323 (mt-10) cc_final: 0.6771 (pp20) REVERT: A 516 GLU cc_start: 0.6694 (tp30) cc_final: 0.5705 (pm20) outliers start: 21 outliers final: 16 residues processed: 114 average time/residue: 0.2229 time to fit residues: 35.1933 Evaluate side-chains 108 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.882 ------------------------------------------------------------------------------- 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 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 131 THR Chi-restraints excluded: chain B residue 381 VAL 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 65 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 69 optimal weight: 0.9990 chunk 62 optimal weight: 20.0000 chunk 35 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 53 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 44 optimal weight: 30.0000 chunk 95 optimal weight: 10.0000 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 = 0.4309 r_free = 0.4309 target = 0.205206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.166069 restraints weight = 9786.565| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 2.08 r_work: 0.3730 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.1873 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= 0.308 Angle : 0.620 6.797 12231 Z= 0.322 Chirality : 0.044 0.151 1329 Planarity : 0.006 0.055 1421 Dihedral : 14.992 85.415 1377 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 2.21 % Allowed : 18.04 % 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: -0.77 (0.28), residues: 951 helix: 0.86 (0.30), residues: 315 sheet: -1.06 (0.38), residues: 178 loop : -1.23 (0.29), 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 0.013 0.002 PHE A 227 TYR 0.020 0.002 TYR B 144 ARG 0.003 0.000 ARG A 358 *********************** 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: 19 poor density : 99 time to evaluate : 0.877 Fit side-chains REVERT: A 47 ILE cc_start: 0.7650 (mm) cc_final: 0.7232 (mt) REVERT: A 514 GLU cc_start: 0.7492 (mt-10) cc_final: 0.6808 (pp20) REVERT: A 516 GLU cc_start: 0.6607 (tp30) cc_final: 0.5659 (pm20) REVERT: B 181 TYR cc_start: 0.7743 (t80) cc_final: 0.7396 (t80) outliers start: 19 outliers final: 18 residues processed: 115 average time/residue: 0.2243 time to fit residues: 35.8135 Evaluate side-chains 112 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 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 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: 7.9990 chunk 9 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 6 optimal weight: 20.0000 chunk 91 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 95 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 40.0000 chunk 84 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 = 0.4336 r_free = 0.4336 target = 0.207468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.169302 restraints weight = 9830.035| |-----------------------------------------------------------------------------| r_work (start): 0.3974 rms_B_bonded: 2.09 r_work: 0.3715 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.1877 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= 0.279 Angle : 0.608 6.735 12231 Z= 0.315 Chirality : 0.043 0.150 1329 Planarity : 0.005 0.055 1421 Dihedral : 14.965 85.203 1377 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 2.44 % Allowed : 18.16 % Favored : 79.39 % 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: -0.71 (0.28), residues: 951 helix: 0.93 (0.30), residues: 315 sheet: -1.02 (0.38), residues: 178 loop : -1.20 (0.30), residues: 458 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 0.018 0.002 TYR B 144 ARG 0.002 0.000 ARG A 358 *********************** 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 117 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 1.024 Fit side-chains REVERT: A 47 ILE cc_start: 0.7633 (mm) cc_final: 0.7214 (mt) REVERT: A 516 GLU cc_start: 0.6643 (tp30) cc_final: 0.5657 (pm20) REVERT: B 181 TYR cc_start: 0.7744 (t80) cc_final: 0.7375 (t80) outliers start: 21 outliers final: 20 residues processed: 112 average time/residue: 0.2158 time to fit residues: 33.3698 Evaluate side-chains 111 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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 357 MET Chi-restraints excluded: chain B residue 422 LEU 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: 0.0670 chunk 67 optimal weight: 7.9990 chunk 87 optimal weight: 0.7980 chunk 9 optimal weight: 9.9990 chunk 22 optimal weight: 0.9990 chunk 32 optimal weight: 10.0000 chunk 86 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 42 optimal weight: 5.9990 chunk 92 optimal weight: 10.0000 chunk 44 optimal weight: 40.0000 overall best weight: 1.5122 ------------------------------------------------------------------------------- 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 = 0.4355 r_free = 0.4355 target = 0.210219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.171416 restraints weight = 9688.553| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 2.15 r_work: 0.3732 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.1741 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= 0.172 Angle : 0.541 6.337 12231 Z= 0.278 Chirality : 0.040 0.145 1329 Planarity : 0.005 0.055 1421 Dihedral : 14.631 81.676 1377 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.40 % Allowed : 19.09 % 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: -0.33 (0.28), residues: 951 helix: 1.35 (0.31), residues: 319 sheet: -0.77 (0.39), residues: 177 loop : -1.11 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 402 HIS 0.004 0.001 HIS B 208 PHE 0.010 0.001 PHE B 77 TYR 0.015 0.001 TYR A 144 ARG 0.001 0.000 ARG A 125 *********************** 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 116 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.896 Fit side-chains REVERT: A 115 TYR cc_start: 0.7521 (t80) cc_final: 0.6651 (t80) REVERT: A 516 GLU cc_start: 0.6457 (tp30) cc_final: 0.5609 (pm20) outliers start: 12 outliers final: 10 residues processed: 112 average time/residue: 0.2197 time to fit residues: 34.1953 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 : 0.858 ------------------------------------------------------------------------------- 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 493 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 357 MET 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: 3.9990 chunk 68 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 7 optimal weight: 10.0000 chunk 77 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 = 0.4328 r_free = 0.4328 target = 0.207530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.169356 restraints weight = 9692.421| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 2.22 r_work: 0.3706 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8890 Z= 0.235 Angle : 0.582 7.904 12231 Z= 0.299 Chirality : 0.042 0.144 1329 Planarity : 0.005 0.054 1421 Dihedral : 14.709 82.503 1377 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.86 % Allowed : 18.98 % Favored : 79.16 % 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: -0.41 (0.28), residues: 951 helix: 1.21 (0.30), residues: 321 sheet: -0.75 (0.39), residues: 176 loop : -1.14 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 402 HIS 0.004 0.001 HIS B 208 PHE 0.009 0.001 PHE B 130 TYR 0.016 0.002 TYR B 144 ARG 0.002 0.000 ARG A 358 ********************** 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 114 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.996 Fit side-chains REVERT: A 516 GLU cc_start: 0.6547 (tp30) cc_final: 0.5642 (pm20) outliers start: 16 outliers final: 14 residues processed: 109 average time/residue: 0.2102 time to fit residues: 32.4250 Evaluate side-chains 111 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.858 ------------------------------------------------------------------------------- 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 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 113 ASP Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 357 MET Chi-restraints excluded: chain B residue 381 VAL 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: 6.9990 chunk 97 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 67 optimal weight: 8.9990 chunk 38 optimal weight: 0.0670 chunk 93 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 chunk 43 optimal weight: 8.9990 chunk 17 optimal weight: 10.0000 chunk 87 optimal weight: 0.9990 overall best weight: 2.8126 ------------------------------------------------------------------------------- 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 = 0.4335 r_free = 0.4335 target = 0.208225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.169983 restraints weight = 9695.617| |-----------------------------------------------------------------------------| r_work (start): 0.4018 rms_B_bonded: 2.17 r_work: 0.3759 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8890 Z= 0.205 Angle : 0.569 8.104 12231 Z= 0.292 Chirality : 0.041 0.142 1329 Planarity : 0.005 0.054 1421 Dihedral : 14.684 82.268 1377 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 1.63 % Allowed : 19.21 % Favored : 79.16 % 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: -0.39 (0.28), residues: 951 helix: 1.24 (0.30), residues: 321 sheet: -0.78 (0.39), residues: 178 loop : -1.13 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 402 HIS 0.004 0.001 HIS B 208 PHE 0.009 0.001 PHE A 227 TYR 0.013 0.001 TYR B 144 ARG 0.001 0.000 ARG A 358 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3635.75 seconds wall clock time: 65 minutes 33.20 seconds (3933.20 seconds total)