Starting phenix.real_space_refine on Fri Oct 10 11:48:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jtw_36654/10_2025/8jtw_36654.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jtw_36654/10_2025/8jtw_36654.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jtw_36654/10_2025/8jtw_36654.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jtw_36654/10_2025/8jtw_36654.map" model { file = "/net/cci-nas-00/data/ceres_data/8jtw_36654/10_2025/8jtw_36654.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jtw_36654/10_2025/8jtw_36654.cif" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.004 sd= 0.179 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 34 5.16 5 C 2793 2.51 5 N 705 2.21 5 O 750 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4282 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3370 Classifications: {'peptide': 448} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 22, 'TRANS': 425} Chain breaks: 1 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 3, 'ARG:plan': 2, 'PHE:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "B" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 912 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 114} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 1.30, per 1000 atoms: 0.30 Number of scatterers: 4282 At special positions: 0 Unit cell: (60.2, 79.98, 125.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 34 16.00 O 750 8.00 N 705 7.00 C 2793 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 121 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 102 " distance=2.03 Simple disulfide: pdb=" SG CYS A 88 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.38 Conformation dependent library (CDL) restraints added in 104.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1024 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 3 sheets defined 62.2% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 21 through 38 removed outlier: 4.263A pdb=" N LEU A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA A 33 " --> pdb=" O SER A 29 " (cutoff:3.500A) Proline residue: A 34 - end of helix Processing helix chain 'A' and resid 38 through 43 removed outlier: 3.572A pdb=" N GLY A 43 " --> pdb=" O ILE A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 62 removed outlier: 4.021A pdb=" N LEU A 58 " --> pdb=" O GLY A 54 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N CYS A 62 " --> pdb=" O LEU A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 72 Processing helix chain 'A' and resid 104 through 110 Processing helix chain 'A' and resid 133 through 139 Processing helix chain 'A' and resid 141 through 147 removed outlier: 4.788A pdb=" N TRP A 146 " --> pdb=" O ALA A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 164 removed outlier: 4.192A pdb=" N GLN A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU A 155 " --> pdb=" O PHE A 151 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 173 removed outlier: 3.777A pdb=" N PHE A 169 " --> pdb=" O GLY A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 195 removed outlier: 3.537A pdb=" N CYS A 178 " --> pdb=" O GLY A 174 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU A 179 " --> pdb=" O ARG A 175 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU A 180 " --> pdb=" O LYS A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 228 removed outlier: 3.595A pdb=" N MET A 202 " --> pdb=" O ASN A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 258 removed outlier: 3.519A pdb=" N LEU A 251 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR A 252 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLY A 253 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA A 257 " --> pdb=" O GLY A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 277 Proline residue: A 271 - end of helix Processing helix chain 'A' and resid 333 through 339 removed outlier: 3.740A pdb=" N LEU A 337 " --> pdb=" O PHE A 334 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE A 338 " --> pdb=" O ALA A 335 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ARG A 339 " --> pdb=" O ASP A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 372 removed outlier: 3.598A pdb=" N THR A 347 " --> pdb=" O LEU A 343 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N PHE A 348 " --> pdb=" O ARG A 344 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ILE A 349 " --> pdb=" O LYS A 345 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN A 362 " --> pdb=" O SER A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 386 Processing helix chain 'A' and resid 387 through 396 removed outlier: 4.009A pdb=" N PHE A 391 " --> pdb=" O ILE A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 422 removed outlier: 3.991A pdb=" N MET A 406 " --> pdb=" O ARG A 402 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLY A 414 " --> pdb=" O ASN A 410 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA A 415 " --> pdb=" O LEU A 411 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA A 416 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N CYS A 417 " --> pdb=" O ALA A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 457 removed outlier: 3.627A pdb=" N ILE A 433 " --> pdb=" O TRP A 429 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN A 447 " --> pdb=" O THR A 443 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET A 448 " --> pdb=" O ILE A 444 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE A 449 " --> pdb=" O ALA A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 487 removed outlier: 4.096A pdb=" N SER A 470 " --> pdb=" O VAL A 466 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE A 475 " --> pdb=" O SER A 471 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY A 476 " --> pdb=" O LEU A 472 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE A 479 " --> pdb=" O ILE A 475 " (cutoff:3.500A) Proline residue: A 481 - end of helix Processing helix chain 'A' and resid 493 through 508 removed outlier: 3.603A pdb=" N ILE A 497 " --> pdb=" O ALA A 493 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY A 508 " --> pdb=" O LEU A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 513 Processing helix chain 'B' and resid 27 through 32 removed outlier: 3.588A pdb=" N TYR B 31 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLU B 32 " --> pdb=" O ILE B 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 27 through 32' Processing helix chain 'B' and resid 61 through 64 removed outlier: 3.692A pdb=" N LYS B 64 " --> pdb=" O ASP B 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 61 through 64' Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 50 removed outlier: 3.507A pdb=" N HIS A 49 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 5 through 7 removed outlier: 3.622A pdb=" N MET B 82 " --> pdb=" O LEU B 18 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 59 removed outlier: 3.996A pdb=" N ASN B 58 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL B 48 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N THR B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N MET B 34 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA B 91 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL B 118 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR B 116 " --> pdb=" O TYR B 93 " (cutoff:3.500A) 230 hydrogen bonds defined for protein. 660 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.55 Time building geometry restraints manager: 0.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1344 1.34 - 1.46: 1056 1.46 - 1.58: 1938 1.58 - 1.69: 0 1.69 - 1.81: 51 Bond restraints: 4389 Sorted by residual: bond pdb=" C VAL A 74 " pdb=" O VAL A 74 " ideal model delta sigma weight residual 1.247 1.230 0.017 1.23e-02 6.61e+03 1.90e+00 bond pdb=" CA LEU A 77 " pdb=" C LEU A 77 " ideal model delta sigma weight residual 1.532 1.515 0.017 1.41e-02 5.03e+03 1.49e+00 bond pdb=" CA THR A 45 " pdb=" CB THR A 45 " ideal model delta sigma weight residual 1.530 1.543 -0.013 1.58e-02 4.01e+03 6.50e-01 bond pdb=" N GLY A 78 " pdb=" CA GLY A 78 " ideal model delta sigma weight residual 1.443 1.453 -0.011 1.37e-02 5.33e+03 6.17e-01 bond pdb=" C VAL A 74 " pdb=" N PRO A 75 " ideal model delta sigma weight residual 1.332 1.341 -0.010 1.30e-02 5.92e+03 5.60e-01 ... (remaining 4384 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 5900 1.98 - 3.95: 67 3.95 - 5.93: 15 5.93 - 7.91: 0 7.91 - 9.88: 1 Bond angle restraints: 5983 Sorted by residual: angle pdb=" C LEU A 456 " pdb=" N TYR A 457 " pdb=" CA TYR A 457 " ideal model delta sigma weight residual 122.15 112.27 9.88 3.47e+00 8.31e-02 8.11e+00 angle pdb=" CA VAL A 74 " pdb=" C VAL A 74 " pdb=" N PRO A 75 " ideal model delta sigma weight residual 119.37 116.83 2.54 1.13e+00 7.83e-01 5.07e+00 angle pdb=" N ILE A 387 " pdb=" CA ILE A 387 " pdb=" C ILE A 387 " ideal model delta sigma weight residual 108.88 113.56 -4.68 2.16e+00 2.14e-01 4.69e+00 angle pdb=" CA THR A 45 " pdb=" CB THR A 45 " pdb=" CG2 THR A 45 " ideal model delta sigma weight residual 110.50 114.15 -3.65 1.70e+00 3.46e-01 4.61e+00 angle pdb=" N PRO A 79 " pdb=" CA PRO A 79 " pdb=" C PRO A 79 " ideal model delta sigma weight residual 113.47 110.41 3.06 1.43e+00 4.89e-01 4.58e+00 ... (remaining 5978 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.65: 2298 16.65 - 33.30: 193 33.30 - 49.96: 42 49.96 - 66.61: 6 66.61 - 83.26: 3 Dihedral angle restraints: 2542 sinusoidal: 932 harmonic: 1610 Sorted by residual: dihedral pdb=" CB CYS A 50 " pdb=" SG CYS A 50 " pdb=" SG CYS A 121 " pdb=" CB CYS A 121 " ideal model delta sinusoidal sigma weight residual -86.00 -150.22 64.22 1 1.00e+01 1.00e-02 5.42e+01 dihedral pdb=" CB CYS A 88 " pdb=" SG CYS A 88 " pdb=" SG CYS A 142 " pdb=" CB CYS A 142 " ideal model delta sinusoidal sigma weight residual 93.00 156.81 -63.81 1 1.00e+01 1.00e-02 5.36e+01 dihedral pdb=" CA VAL A 461 " pdb=" C VAL A 461 " pdb=" N ARG A 462 " pdb=" CA ARG A 462 " ideal model delta harmonic sigma weight residual -180.00 -163.63 -16.37 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 2539 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 459 0.034 - 0.068: 167 0.068 - 0.102: 41 0.102 - 0.136: 19 0.136 - 0.170: 1 Chirality restraints: 687 Sorted by residual: chirality pdb=" CB THR A 45 " pdb=" CA THR A 45 " pdb=" OG1 THR A 45 " pdb=" CG2 THR A 45 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.24e-01 chirality pdb=" CA THR A 45 " pdb=" N THR A 45 " pdb=" C THR A 45 " pdb=" CB THR A 45 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.13 2.00e-01 2.50e+01 4.53e-01 chirality pdb=" CA ILE B 51 " pdb=" N ILE B 51 " pdb=" C ILE B 51 " pdb=" CB ILE B 51 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.37e-01 ... (remaining 684 not shown) Planarity restraints: 751 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 460 " -0.009 2.00e-02 2.50e+03 1.83e-02 3.35e+00 pdb=" C PHE A 460 " 0.032 2.00e-02 2.50e+03 pdb=" O PHE A 460 " -0.012 2.00e-02 2.50e+03 pdb=" N VAL A 461 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 461 " 0.008 2.00e-02 2.50e+03 1.61e-02 2.58e+00 pdb=" C VAL A 461 " -0.028 2.00e-02 2.50e+03 pdb=" O VAL A 461 " 0.011 2.00e-02 2.50e+03 pdb=" N ARG A 462 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 387 " -0.017 5.00e-02 4.00e+02 2.58e-02 1.07e+00 pdb=" N PRO A 388 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 388 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 388 " -0.015 5.00e-02 4.00e+02 ... (remaining 748 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1276 2.83 - 3.35: 3838 3.35 - 3.86: 6280 3.86 - 4.38: 6620 4.38 - 4.90: 12477 Nonbonded interactions: 30491 Sorted by model distance: nonbonded pdb=" O GLY A 476 " pdb=" OG1 THR A 480 " model vdw 2.309 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" O TRP B 106 " model vdw 2.329 3.040 nonbonded pdb=" NH1 ARG B 66 " pdb=" O SER B 84 " model vdw 2.424 3.120 nonbonded pdb=" O VAL A 185 " pdb=" OG SER A 189 " model vdw 2.437 3.040 nonbonded pdb=" OD1 ASP B 72 " pdb=" N ASN B 73 " model vdw 2.442 3.120 ... (remaining 30486 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: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.080 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 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 : 0.002 0.027 4393 Z= 0.120 Angle : 0.556 9.884 5991 Z= 0.291 Chirality : 0.040 0.170 687 Planarity : 0.003 0.026 751 Dihedral : 13.050 83.260 1506 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.37), residues: 560 helix: 1.12 (0.31), residues: 318 sheet: 0.81 (0.90), residues: 37 loop : -1.73 (0.42), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 339 TYR 0.010 0.001 TYR A 457 PHE 0.015 0.001 PHE A 275 TRP 0.011 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 4389) covalent geometry : angle 0.55581 ( 5983) SS BOND : bond 0.00144 ( 4) SS BOND : angle 0.26242 ( 8) hydrogen bonds : bond 0.19999 ( 230) hydrogen bonds : angle 5.21117 ( 660) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.147 Fit side-chains revert: symmetry clash REVERT: A 368 MET cc_start: 0.6794 (tmm) cc_final: 0.6575 (ttp) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0701 time to fit residues: 4.5164 Evaluate side-chains 48 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 54 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.4980 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.4980 chunk 50 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 453 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.217478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.164202 restraints weight = 4578.067| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 2.36 r_work: 0.3676 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.1033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4393 Z= 0.120 Angle : 0.537 10.941 5991 Z= 0.268 Chirality : 0.040 0.153 687 Planarity : 0.003 0.036 751 Dihedral : 3.779 15.266 610 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.91 % Allowed : 4.55 % Favored : 94.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.37), residues: 560 helix: 1.35 (0.30), residues: 320 sheet: 0.64 (0.69), residues: 51 loop : -1.61 (0.46), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 339 TYR 0.014 0.001 TYR A 457 PHE 0.015 0.001 PHE A 275 TRP 0.010 0.001 TRP A 261 HIS 0.003 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 4389) covalent geometry : angle 0.53737 ( 5983) SS BOND : bond 0.00122 ( 4) SS BOND : angle 0.36256 ( 8) hydrogen bonds : bond 0.05100 ( 230) hydrogen bonds : angle 4.10847 ( 660) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.168 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 54 average time/residue: 0.0779 time to fit residues: 5.3941 Evaluate side-chains 51 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 385 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 11 optimal weight: 0.6980 chunk 42 optimal weight: 0.4980 chunk 22 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 20 optimal weight: 0.0020 chunk 12 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.216137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.161945 restraints weight = 4513.383| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 2.41 r_work: 0.3662 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4393 Z= 0.116 Angle : 0.515 10.462 5991 Z= 0.259 Chirality : 0.040 0.136 687 Planarity : 0.003 0.037 751 Dihedral : 3.728 14.974 610 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.91 % Allowed : 7.50 % Favored : 91.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.37), residues: 560 helix: 1.51 (0.30), residues: 319 sheet: 0.72 (0.68), residues: 51 loop : -1.84 (0.45), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 339 TYR 0.011 0.001 TYR A 457 PHE 0.009 0.001 PHE A 275 TRP 0.011 0.001 TRP A 261 HIS 0.003 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 4389) covalent geometry : angle 0.51515 ( 5983) SS BOND : bond 0.00111 ( 4) SS BOND : angle 0.26771 ( 8) hydrogen bonds : bond 0.04900 ( 230) hydrogen bonds : angle 3.90569 ( 660) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.153 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 53 average time/residue: 0.0720 time to fit residues: 4.9077 Evaluate side-chains 53 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 385 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 41 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 7 optimal weight: 8.9990 chunk 26 optimal weight: 4.9990 chunk 10 optimal weight: 0.4980 chunk 31 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.206275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.153794 restraints weight = 4493.424| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 2.10 r_work: 0.3559 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3416 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 4393 Z= 0.195 Angle : 0.635 9.222 5991 Z= 0.323 Chirality : 0.044 0.155 687 Planarity : 0.004 0.031 751 Dihedral : 4.211 17.773 610 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 1.36 % Allowed : 10.45 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.36), residues: 560 helix: 1.14 (0.30), residues: 313 sheet: -0.13 (0.66), residues: 57 loop : -2.01 (0.44), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 339 TYR 0.011 0.001 TYR A 457 PHE 0.011 0.001 PHE A 273 TRP 0.012 0.001 TRP A 261 HIS 0.004 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00454 ( 4389) covalent geometry : angle 0.63527 ( 5983) SS BOND : bond 0.00249 ( 4) SS BOND : angle 0.36921 ( 8) hydrogen bonds : bond 0.07583 ( 230) hydrogen bonds : angle 4.39361 ( 660) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.148 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 55 average time/residue: 0.0868 time to fit residues: 5.9015 Evaluate side-chains 51 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain B residue 102 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 47 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.210138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.155207 restraints weight = 4530.710| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 2.31 r_work: 0.3600 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.3452 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4393 Z= 0.135 Angle : 0.545 9.444 5991 Z= 0.278 Chirality : 0.041 0.141 687 Planarity : 0.004 0.033 751 Dihedral : 3.992 16.186 610 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.91 % Allowed : 12.73 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.37), residues: 560 helix: 1.27 (0.30), residues: 317 sheet: -0.14 (0.65), residues: 57 loop : -1.87 (0.46), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 339 TYR 0.011 0.001 TYR A 457 PHE 0.028 0.001 PHE A 460 TRP 0.013 0.001 TRP A 261 HIS 0.003 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 4389) covalent geometry : angle 0.54524 ( 5983) SS BOND : bond 0.00186 ( 4) SS BOND : angle 0.27216 ( 8) hydrogen bonds : bond 0.05634 ( 230) hydrogen bonds : angle 4.09578 ( 660) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.152 Fit side-chains REVERT: A 408 MET cc_start: 0.7692 (tpp) cc_final: 0.7404 (mmm) outliers start: 4 outliers final: 4 residues processed: 51 average time/residue: 0.0867 time to fit residues: 5.5087 Evaluate side-chains 52 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain B residue 102 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 12 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 9.9990 chunk 24 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 30 optimal weight: 0.2980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.212275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.158501 restraints weight = 4554.125| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 2.32 r_work: 0.3624 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3478 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4393 Z= 0.120 Angle : 0.519 9.418 5991 Z= 0.263 Chirality : 0.040 0.142 687 Planarity : 0.003 0.031 751 Dihedral : 3.864 15.289 610 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.14 % Allowed : 14.32 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.37), residues: 560 helix: 1.46 (0.30), residues: 316 sheet: 0.00 (0.66), residues: 57 loop : -1.77 (0.46), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 339 TYR 0.011 0.001 TYR A 457 PHE 0.024 0.001 PHE A 460 TRP 0.012 0.001 TRP A 261 HIS 0.003 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 4389) covalent geometry : angle 0.51910 ( 5983) SS BOND : bond 0.00158 ( 4) SS BOND : angle 0.22658 ( 8) hydrogen bonds : bond 0.04984 ( 230) hydrogen bonds : angle 3.93428 ( 660) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.147 Fit side-chains REVERT: A 160 LEU cc_start: 0.6628 (tt) cc_final: 0.6392 (tp) REVERT: A 408 MET cc_start: 0.7710 (tpp) cc_final: 0.7494 (mmm) outliers start: 5 outliers final: 4 residues processed: 52 average time/residue: 0.0858 time to fit residues: 5.6004 Evaluate side-chains 52 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain B residue 102 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 37 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.207646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.153068 restraints weight = 4529.222| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 2.32 r_work: 0.3523 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4393 Z= 0.135 Angle : 0.538 8.994 5991 Z= 0.274 Chirality : 0.041 0.142 687 Planarity : 0.004 0.032 751 Dihedral : 3.930 15.656 610 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 1.14 % Allowed : 14.32 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.37), residues: 560 helix: 1.51 (0.31), residues: 310 sheet: -0.20 (0.62), residues: 64 loop : -1.83 (0.46), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 339 TYR 0.011 0.001 TYR A 457 PHE 0.019 0.001 PHE A 460 TRP 0.012 0.001 TRP A 261 HIS 0.003 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 4389) covalent geometry : angle 0.53857 ( 5983) SS BOND : bond 0.00186 ( 4) SS BOND : angle 0.23910 ( 8) hydrogen bonds : bond 0.05554 ( 230) hydrogen bonds : angle 4.01355 ( 660) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.154 Fit side-chains REVERT: B 46 GLU cc_start: 0.7399 (tt0) cc_final: 0.7190 (tt0) outliers start: 5 outliers final: 4 residues processed: 53 average time/residue: 0.0794 time to fit residues: 5.2148 Evaluate side-chains 53 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain B residue 102 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 24 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 43 optimal weight: 0.1980 chunk 27 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 7 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.209017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.154889 restraints weight = 4515.025| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 2.26 r_work: 0.3552 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4393 Z= 0.124 Angle : 0.524 8.997 5991 Z= 0.266 Chirality : 0.040 0.140 687 Planarity : 0.003 0.031 751 Dihedral : 3.868 15.218 610 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.14 % Allowed : 14.55 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.37), residues: 560 helix: 1.55 (0.31), residues: 312 sheet: -0.19 (0.62), residues: 64 loop : -1.72 (0.46), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 339 TYR 0.011 0.001 TYR A 457 PHE 0.019 0.001 PHE A 460 TRP 0.012 0.001 TRP A 261 HIS 0.003 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 4389) covalent geometry : angle 0.52418 ( 5983) SS BOND : bond 0.00168 ( 4) SS BOND : angle 0.22749 ( 8) hydrogen bonds : bond 0.05094 ( 230) hydrogen bonds : angle 3.95166 ( 660) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.118 Fit side-chains REVERT: A 160 LEU cc_start: 0.6585 (tt) cc_final: 0.6333 (tp) REVERT: A 275 PHE cc_start: 0.5600 (OUTLIER) cc_final: 0.5045 (m-10) REVERT: A 408 MET cc_start: 0.7781 (tpp) cc_final: 0.7567 (mmm) outliers start: 5 outliers final: 4 residues processed: 53 average time/residue: 0.0796 time to fit residues: 5.2443 Evaluate side-chains 53 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain B residue 102 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 27 optimal weight: 1.9990 chunk 43 optimal weight: 0.1980 chunk 41 optimal weight: 0.0270 chunk 22 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.211118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.157396 restraints weight = 4546.376| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 2.26 r_work: 0.3576 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4393 Z= 0.111 Angle : 0.511 9.024 5991 Z= 0.258 Chirality : 0.040 0.137 687 Planarity : 0.003 0.031 751 Dihedral : 3.781 14.302 610 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.36 % Allowed : 14.55 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.37), residues: 560 helix: 1.55 (0.31), residues: 319 sheet: -0.16 (0.62), residues: 64 loop : -1.63 (0.48), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 339 TYR 0.011 0.001 TYR A 457 PHE 0.019 0.001 PHE A 460 TRP 0.012 0.001 TRP A 261 HIS 0.003 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 4389) covalent geometry : angle 0.51089 ( 5983) SS BOND : bond 0.00134 ( 4) SS BOND : angle 0.21286 ( 8) hydrogen bonds : bond 0.04455 ( 230) hydrogen bonds : angle 3.83411 ( 660) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.257 Fit side-chains REVERT: A 275 PHE cc_start: 0.5723 (OUTLIER) cc_final: 0.5104 (m-10) REVERT: A 408 MET cc_start: 0.7530 (tpp) cc_final: 0.7187 (mmm) outliers start: 6 outliers final: 3 residues processed: 51 average time/residue: 0.0793 time to fit residues: 5.1848 Evaluate side-chains 50 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain B residue 102 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 36 optimal weight: 0.9990 chunk 8 optimal weight: 10.0000 chunk 6 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 24 optimal weight: 0.0970 chunk 19 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.209700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.155312 restraints weight = 4548.826| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 2.28 r_work: 0.3555 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4393 Z= 0.122 Angle : 0.528 8.777 5991 Z= 0.267 Chirality : 0.040 0.141 687 Planarity : 0.003 0.031 751 Dihedral : 3.811 14.857 610 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 0.91 % Allowed : 15.68 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.37), residues: 560 helix: 1.55 (0.31), residues: 318 sheet: -0.17 (0.62), residues: 64 loop : -1.68 (0.47), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 339 TYR 0.012 0.001 TYR A 457 PHE 0.017 0.001 PHE A 460 TRP 0.012 0.001 TRP A 261 HIS 0.003 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 4389) covalent geometry : angle 0.52808 ( 5983) SS BOND : bond 0.00164 ( 4) SS BOND : angle 0.22763 ( 8) hydrogen bonds : bond 0.04890 ( 230) hydrogen bonds : angle 3.91103 ( 660) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.168 Fit side-chains REVERT: A 275 PHE cc_start: 0.5684 (OUTLIER) cc_final: 0.5143 (m-10) REVERT: A 408 MET cc_start: 0.7518 (tpp) cc_final: 0.7167 (mmm) outliers start: 4 outliers final: 3 residues processed: 50 average time/residue: 0.0661 time to fit residues: 4.2596 Evaluate side-chains 51 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain B residue 102 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 10 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 34 optimal weight: 0.0270 chunk 6 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 7 optimal weight: 6.9990 overall best weight: 1.0440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.205657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.150805 restraints weight = 4479.920| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 2.30 r_work: 0.3505 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4393 Z= 0.154 Angle : 0.573 8.530 5991 Z= 0.292 Chirality : 0.042 0.146 687 Planarity : 0.004 0.032 751 Dihedral : 4.015 16.701 610 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 1.36 % Allowed : 15.23 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.37), residues: 560 helix: 1.31 (0.30), residues: 319 sheet: -0.21 (0.62), residues: 64 loop : -1.78 (0.47), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 339 TYR 0.011 0.001 TYR A 457 PHE 0.012 0.001 PHE A 460 TRP 0.012 0.001 TRP A 261 HIS 0.004 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 4389) covalent geometry : angle 0.57340 ( 5983) SS BOND : bond 0.00215 ( 4) SS BOND : angle 0.28448 ( 8) hydrogen bonds : bond 0.06109 ( 230) hydrogen bonds : angle 4.15813 ( 660) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1291.86 seconds wall clock time: 22 minutes 44.55 seconds (1364.55 seconds total)