Starting phenix.real_space_refine on Thu Jul 2 05:04:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8un2_42391/07_2026/8un2_42391.cif Found real_map, /net/cci-nas-00/data/ceres_data/8un2_42391/07_2026/8un2_42391.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8un2_42391/07_2026/8un2_42391.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8un2_42391/07_2026/8un2_42391.map" model { file = "/net/cci-nas-00/data/ceres_data/8un2_42391/07_2026/8un2_42391.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8un2_42391/07_2026/8un2_42391.cif" } resolution = 2.3 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= 0.001 sd= 0.025 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 Mn 2 7.51 5 S 20 5.16 5 C 4378 2.51 5 N 1172 2.21 5 O 1282 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6854 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3426 Classifications: {'peptide': 433} Link IDs: {'PCIS': 4, 'PTRANS': 29, 'TRANS': 399} Chain: "B" Number of atoms: 3426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3426 Classifications: {'peptide': 433} Link IDs: {'PCIS': 4, 'PTRANS': 29, 'TRANS': 399} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' MN': 1} Chain breaks: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' MN': 1} Chain breaks: 1 Time building chain proxies: 1.69, per 1000 atoms: 0.25 Number of scatterers: 6854 At special positions: 0 Unit cell: (92.3832, 108.626, 68.0184, 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) Mn 2 24.99 S 20 16.00 O 1282 8.00 N 1172 7.00 C 4378 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.58 Conformation dependent library (CDL) restraints added in 466.8 milliseconds 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1584 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 8 sheets defined 34.9% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 70 through 77 Processing helix chain 'A' and resid 117 through 121 Processing helix chain 'A' and resid 149 through 151 No H-bonds generated for 'chain 'A' and resid 149 through 151' Processing helix chain 'A' and resid 160 through 171 Processing helix chain 'A' and resid 180 through 184 Processing helix chain 'A' and resid 191 through 206 removed outlier: 3.524A pdb=" N SER A 203 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 250 removed outlier: 3.568A pdb=" N ALA A 238 " --> pdb=" O GLU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 286 removed outlier: 3.670A pdb=" N GLU A 276 " --> pdb=" O THR A 272 " (cutoff:3.500A) Proline residue: A 280 - end of helix Processing helix chain 'A' and resid 301 through 315 Processing helix chain 'A' and resid 326 through 329 Processing helix chain 'A' and resid 345 through 350 removed outlier: 3.596A pdb=" N ASP A 349 " --> pdb=" O ALA A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 360 removed outlier: 3.555A pdb=" N VAL A 358 " --> pdb=" O PRO A 355 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASP A 360 " --> pdb=" O ASP A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 396 Processing helix chain 'A' and resid 413 through 433 removed outlier: 4.141A pdb=" N GLU A 417 " --> pdb=" O TRP A 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 77 Processing helix chain 'B' and resid 117 through 121 Processing helix chain 'B' and resid 149 through 151 No H-bonds generated for 'chain 'B' and resid 149 through 151' Processing helix chain 'B' and resid 160 through 171 Processing helix chain 'B' and resid 180 through 184 Processing helix chain 'B' and resid 191 through 206 removed outlier: 3.524A pdb=" N SER B 203 " --> pdb=" O PHE B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 250 removed outlier: 3.569A pdb=" N ALA B 238 " --> pdb=" O GLU B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 286 removed outlier: 3.670A pdb=" N GLU B 276 " --> pdb=" O THR B 272 " (cutoff:3.500A) Proline residue: B 280 - end of helix Processing helix chain 'B' and resid 301 through 315 Processing helix chain 'B' and resid 326 through 329 Processing helix chain 'B' and resid 345 through 350 removed outlier: 3.596A pdb=" N ASP B 349 " --> pdb=" O ALA B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 360 removed outlier: 3.556A pdb=" N VAL B 358 " --> pdb=" O PRO B 355 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP B 360 " --> pdb=" O ASP B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 396 Processing helix chain 'B' and resid 413 through 433 removed outlier: 4.142A pdb=" N GLU B 417 " --> pdb=" O TRP B 413 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 18 removed outlier: 3.671A pdb=" N GLY A 24 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N GLU A 18 " --> pdb=" O ILE A 22 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ILE A 22 " --> pdb=" O GLU A 18 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE A 89 " --> pdb=" O THR A 63 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 37 through 38 Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.640A pdb=" N GLY A 44 " --> pdb=" O ARG A 110 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL A 127 " --> pdb=" O ILE A 107 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 288 through 289 removed outlier: 7.582A pdb=" N ILE A 176 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N MET A 212 " --> pdb=" O ILE A 176 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ILE A 178 " --> pdb=" O MET A 212 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N SER A 214 " --> pdb=" O ILE A 178 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N TYR A 144 " --> pdb=" O GLY A 175 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N GLU A 177 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL A 146 " --> pdb=" O GLU A 177 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N LEU A 179 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N TYR A 406 " --> pdb=" O SER A 147 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N TYR A 401 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A 368 " --> pdb=" O TYR A 401 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N LEU A 321 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ILE A 368 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEU A 323 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ALA A 370 " --> pdb=" O LEU A 323 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE A 293 " --> pdb=" O ASP A 324 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 14 through 18 removed outlier: 3.672A pdb=" N GLY B 24 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N GLU B 18 " --> pdb=" O ILE B 22 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ILE B 22 " --> pdb=" O GLU B 18 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE B 89 " --> pdb=" O THR B 63 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 37 through 38 Processing sheet with id=AA7, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.641A pdb=" N GLY B 44 " --> pdb=" O ARG B 110 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL B 127 " --> pdb=" O ILE B 107 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 288 through 289 removed outlier: 7.582A pdb=" N ILE B 176 " --> pdb=" O THR B 210 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N MET B 212 " --> pdb=" O ILE B 176 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ILE B 178 " --> pdb=" O MET B 212 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N SER B 214 " --> pdb=" O ILE B 178 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N TYR B 144 " --> pdb=" O GLY B 175 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N GLU B 177 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL B 146 " --> pdb=" O GLU B 177 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N LEU B 179 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N TYR B 406 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N TYR B 401 " --> pdb=" O VAL B 366 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE B 368 " --> pdb=" O TYR B 401 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N LEU B 321 " --> pdb=" O VAL B 366 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ILE B 368 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEU B 323 " --> pdb=" O ILE B 368 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ALA B 370 " --> pdb=" O LEU B 323 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE B 293 " --> pdb=" O ASP B 324 " (cutoff:3.500A) 278 hydrogen bonds defined for protein. 744 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: 0.98 Time building geometry restraints manager: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2204 1.33 - 1.45: 989 1.45 - 1.57: 3801 1.57 - 1.69: 0 1.69 - 1.80: 38 Bond restraints: 7032 Sorted by residual: bond pdb=" CB ARG B 5 " pdb=" CG ARG B 5 " ideal model delta sigma weight residual 1.520 1.459 0.061 3.00e-02 1.11e+03 4.18e+00 bond pdb=" CB ARG A 5 " pdb=" CG ARG A 5 " ideal model delta sigma weight residual 1.520 1.459 0.061 3.00e-02 1.11e+03 4.18e+00 bond pdb=" CB VAL B 254 " pdb=" CG2 VAL B 254 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.71e+00 bond pdb=" CB VAL A 254 " pdb=" CG2 VAL A 254 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.63e+00 bond pdb=" CB PRO B 122 " pdb=" CG PRO B 122 " ideal model delta sigma weight residual 1.506 1.449 0.057 3.90e-02 6.57e+02 2.11e+00 ... (remaining 7027 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 9021 1.49 - 2.98: 467 2.98 - 4.46: 76 4.46 - 5.95: 12 5.95 - 7.44: 8 Bond angle restraints: 9584 Sorted by residual: angle pdb=" C PRO B 412 " pdb=" N TRP B 413 " pdb=" CA TRP B 413 " ideal model delta sigma weight residual 123.91 130.05 -6.14 1.66e+00 3.63e-01 1.37e+01 angle pdb=" C PRO A 412 " pdb=" N TRP A 413 " pdb=" CA TRP A 413 " ideal model delta sigma weight residual 123.91 130.03 -6.12 1.66e+00 3.63e-01 1.36e+01 angle pdb=" CA PRO B 60 " pdb=" N PRO B 60 " pdb=" CD PRO B 60 " ideal model delta sigma weight residual 112.00 108.19 3.81 1.40e+00 5.10e-01 7.39e+00 angle pdb=" CA PRO A 60 " pdb=" N PRO A 60 " pdb=" CD PRO A 60 " ideal model delta sigma weight residual 112.00 108.23 3.77 1.40e+00 5.10e-01 7.26e+00 angle pdb=" CA VAL A 59 " pdb=" C VAL A 59 " pdb=" N PRO A 60 " ideal model delta sigma weight residual 118.88 122.91 -4.03 1.54e+00 4.22e-01 6.86e+00 ... (remaining 9579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.57: 3756 16.57 - 33.13: 338 33.13 - 49.70: 78 49.70 - 66.26: 18 66.26 - 82.83: 10 Dihedral angle restraints: 4200 sinusoidal: 1724 harmonic: 2476 Sorted by residual: dihedral pdb=" CA ILE B 178 " pdb=" C ILE B 178 " pdb=" N LEU B 179 " pdb=" CA LEU B 179 " ideal model delta harmonic sigma weight residual 180.00 161.57 18.43 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA ALA A 134 " pdb=" C ALA A 134 " pdb=" N PRO A 135 " pdb=" CA PRO A 135 " ideal model delta harmonic sigma weight residual -180.00 -161.60 -18.40 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA ILE A 178 " pdb=" C ILE A 178 " pdb=" N LEU A 179 " pdb=" CA LEU A 179 " ideal model delta harmonic sigma weight residual 180.00 161.60 18.40 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 4197 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 531 0.035 - 0.070: 333 0.070 - 0.105: 120 0.105 - 0.140: 49 0.140 - 0.174: 15 Chirality restraints: 1048 Sorted by residual: chirality pdb=" CA GLU A 387 " pdb=" N GLU A 387 " pdb=" C GLU A 387 " pdb=" CB GLU A 387 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.61e-01 chirality pdb=" CA GLU B 387 " pdb=" N GLU B 387 " pdb=" C GLU B 387 " pdb=" CB GLU B 387 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.10e-01 chirality pdb=" CB ILE A 176 " pdb=" CA ILE A 176 " pdb=" CG1 ILE A 176 " pdb=" CG2 ILE A 176 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.54e-01 ... (remaining 1045 not shown) Planarity restraints: 1260 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 279 " 0.051 5.00e-02 4.00e+02 7.60e-02 9.25e+00 pdb=" N PRO B 280 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO B 280 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 280 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 279 " -0.050 5.00e-02 4.00e+02 7.56e-02 9.15e+00 pdb=" N PRO A 280 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO A 280 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 280 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 340 " 0.036 5.00e-02 4.00e+02 5.38e-02 4.63e+00 pdb=" N PRO A 341 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 341 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 341 " 0.030 5.00e-02 4.00e+02 ... (remaining 1257 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 40 2.59 - 3.17: 5243 3.17 - 3.74: 10501 3.74 - 4.32: 16114 4.32 - 4.90: 26060 Nonbonded interactions: 57958 Sorted by model distance: nonbonded pdb=" OE2 GLU A 292 " pdb="MN MN A 501 " model vdw 2.009 3.060 nonbonded pdb=" OE2 GLU B 292 " pdb="MN MN B 501 " model vdw 2.014 3.060 nonbonded pdb=" OE1 GLN A 369 " pdb="MN MN A 501 " model vdw 2.155 3.060 nonbonded pdb=" OE1 GLN B 369 " pdb="MN MN B 501 " model vdw 2.164 3.060 nonbonded pdb=" OD2 ASP B 324 " pdb="MN MN B 501 " model vdw 2.196 3.060 ... (remaining 57953 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 1.090 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.240 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 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 : 0.009 0.061 7032 Z= 0.378 Angle : 0.795 7.438 9584 Z= 0.461 Chirality : 0.054 0.174 1048 Planarity : 0.008 0.076 1260 Dihedral : 14.149 82.828 2616 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.74 (0.25), residues: 862 helix: -4.08 (0.13), residues: 230 sheet: -0.94 (0.41), residues: 154 loop : -0.81 (0.26), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 5 TYR 0.019 0.002 TYR A 144 PHE 0.013 0.002 PHE A 347 TRP 0.014 0.003 TRP B 198 HIS 0.010 0.002 HIS A 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00910 / 0.38 ( 7032) covalent geometry : angle 0.79500 / 0.46 ( 9584) hydrogen bonds : bond 0.27668 / 18.46 ( 278) hydrogen bonds : angle 9.07532 / 6.09 ( 744) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.245 Fit side-chains REVERT: A 43 ASP cc_start: 0.7893 (t70) cc_final: 0.7591 (m-30) REVERT: A 119 GLU cc_start: 0.7450 (pm20) cc_final: 0.7136 (pm20) REVERT: A 126 ARG cc_start: 0.7975 (mtt-85) cc_final: 0.7690 (mtt-85) REVERT: A 273 GLU cc_start: 0.7066 (pm20) cc_final: 0.6475 (pm20) REVERT: A 276 GLU cc_start: 0.7560 (mt-10) cc_final: 0.7126 (mt-10) REVERT: A 286 ASP cc_start: 0.7718 (t70) cc_final: 0.7445 (t0) REVERT: A 349 ASP cc_start: 0.7296 (m-30) cc_final: 0.7054 (m-30) REVERT: A 391 LYS cc_start: 0.7802 (tttm) cc_final: 0.7537 (tttm) REVERT: A 428 GLN cc_start: 0.7918 (mt0) cc_final: 0.7485 (mt0) REVERT: B 21 GLU cc_start: 0.7376 (mm-30) cc_final: 0.7141 (mm-30) REVERT: B 118 GLN cc_start: 0.7459 (tp40) cc_final: 0.7125 (mm-40) REVERT: B 119 GLU cc_start: 0.7410 (pm20) cc_final: 0.6998 (pm20) REVERT: B 159 MET cc_start: 0.8620 (ttm) cc_final: 0.8350 (ttp) REVERT: B 192 ASP cc_start: 0.8022 (m-30) cc_final: 0.7747 (m-30) REVERT: B 241 ARG cc_start: 0.7833 (ttp-170) cc_final: 0.7544 (ttp-170) REVERT: B 257 LYS cc_start: 0.8274 (tppp) cc_final: 0.8036 (tptm) REVERT: B 273 GLU cc_start: 0.6856 (pm20) cc_final: 0.6465 (pm20) REVERT: B 276 GLU cc_start: 0.7513 (mt-10) cc_final: 0.7264 (mt-10) REVERT: B 377 GLU cc_start: 0.7130 (mp0) cc_final: 0.6816 (mp0) REVERT: B 431 ASP cc_start: 0.7113 (m-30) cc_final: 0.6814 (m-30) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.7442 time to fit residues: 123.4971 Evaluate side-chains 140 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.2980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 GLN A 121 GLN A 186 ASN A 221 HIS A 343 GLN A 356 ASN A 369 GLN A 423 HIS B 121 GLN B 221 HIS B 343 GLN B 423 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.113291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.103025 restraints weight = 8504.797| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.35 r_work: 0.3313 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7032 Z= 0.137 Angle : 0.536 5.070 9584 Z= 0.282 Chirality : 0.045 0.141 1048 Planarity : 0.006 0.043 1260 Dihedral : 4.814 17.445 950 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.08 % Allowed : 11.22 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.26), residues: 862 helix: -0.85 (0.27), residues: 256 sheet: -0.62 (0.42), residues: 154 loop : -0.34 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 17 TYR 0.014 0.001 TYR B 144 PHE 0.011 0.001 PHE B 347 TRP 0.017 0.002 TRP A 198 HIS 0.003 0.001 HIS B 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 7032) covalent geometry : angle 0.53622 / 0.28 ( 9584) hydrogen bonds : bond 0.04114 / 2.80 ( 278) hydrogen bonds : angle 5.69388 / 3.73 ( 744) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 169 time to evaluate : 0.248 Fit side-chains REVERT: A 300 LYS cc_start: 0.8210 (mmtp) cc_final: 0.7989 (mmtp) REVERT: B 31 MET cc_start: 0.8715 (tpt) cc_final: 0.8455 (tpt) REVERT: B 233 GLU cc_start: 0.7768 (mp0) cc_final: 0.7509 (mp0) REVERT: B 242 ASP cc_start: 0.7464 (m-30) cc_final: 0.7257 (m-30) outliers start: 8 outliers final: 3 residues processed: 172 average time/residue: 0.7307 time to fit residues: 130.4312 Evaluate side-chains 157 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 154 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 GLN Chi-restraints excluded: chain B residue 343 GLN Chi-restraints excluded: chain B residue 394 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 45 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 GLN A 422 GLN A 428 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.110243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.100028 restraints weight = 8391.732| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.35 r_work: 0.3290 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7032 Z= 0.175 Angle : 0.545 5.160 9584 Z= 0.285 Chirality : 0.047 0.136 1048 Planarity : 0.005 0.035 1260 Dihedral : 4.774 17.408 950 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.89 % Allowed : 13.11 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.27), residues: 862 helix: 0.81 (0.30), residues: 256 sheet: -0.50 (0.42), residues: 154 loop : -0.05 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 17 TYR 0.016 0.001 TYR B 144 PHE 0.012 0.001 PHE A 347 TRP 0.012 0.002 TRP B 198 HIS 0.003 0.001 HIS A 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 ( 7032) covalent geometry : angle 0.54517 / 0.29 ( 9584) hydrogen bonds : bond 0.04596 / 3.11 ( 278) hydrogen bonds : angle 5.33350 / 3.51 ( 744) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 158 time to evaluate : 0.262 Fit side-chains REVERT: A 273 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6770 (mp0) REVERT: A 300 LYS cc_start: 0.8242 (mmtp) cc_final: 0.8034 (mmtp) REVERT: B 67 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.7675 (tm-30) REVERT: B 242 ASP cc_start: 0.7516 (m-30) cc_final: 0.7290 (m-30) REVERT: B 405 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7670 (tt0) outliers start: 14 outliers final: 4 residues processed: 163 average time/residue: 0.6987 time to fit residues: 118.1101 Evaluate side-chains 154 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 148 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain A residue 394 LYS Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 300 LYS Chi-restraints excluded: chain B residue 363 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 61 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 81 optimal weight: 0.0980 chunk 6 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 GLN A 428 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.111250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.101132 restraints weight = 8485.881| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 1.35 r_work: 0.3308 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7032 Z= 0.141 Angle : 0.519 7.539 9584 Z= 0.267 Chirality : 0.046 0.135 1048 Planarity : 0.005 0.041 1260 Dihedral : 4.588 17.902 950 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.76 % Allowed : 13.78 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.28), residues: 862 helix: 1.47 (0.31), residues: 256 sheet: -0.32 (0.43), residues: 154 loop : 0.14 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 17 TYR 0.014 0.001 TYR A 144 PHE 0.011 0.001 PHE B 347 TRP 0.013 0.001 TRP B 198 HIS 0.003 0.001 HIS B 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 ( 7032) covalent geometry : angle 0.51878 / 0.27 ( 9584) hydrogen bonds : bond 0.03944 / 2.67 ( 278) hydrogen bonds : angle 5.12021 / 3.35 ( 744) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 152 time to evaluate : 0.193 Fit side-chains REVERT: A 273 GLU cc_start: 0.7117 (OUTLIER) cc_final: 0.6874 (mp0) REVERT: B 242 ASP cc_start: 0.7497 (m-30) cc_final: 0.7260 (m-30) REVERT: B 369 GLN cc_start: 0.8541 (mt0) cc_final: 0.8341 (mt0) REVERT: B 405 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7576 (tt0) outliers start: 13 outliers final: 6 residues processed: 157 average time/residue: 0.7254 time to fit residues: 117.8754 Evaluate side-chains 158 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 151 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain A residue 394 LYS Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 300 LYS Chi-restraints excluded: chain B residue 363 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 47 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 9 optimal weight: 0.0040 chunk 36 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 46 optimal weight: 0.3980 chunk 54 optimal weight: 0.6980 overall best weight: 0.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 GLN A 428 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.110865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.100734 restraints weight = 8514.570| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.36 r_work: 0.3303 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7032 Z= 0.159 Angle : 0.530 7.077 9584 Z= 0.273 Chirality : 0.047 0.136 1048 Planarity : 0.005 0.038 1260 Dihedral : 4.638 18.592 950 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 2.03 % Allowed : 14.32 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.28), residues: 862 helix: 1.78 (0.31), residues: 256 sheet: -0.24 (0.43), residues: 154 loop : 0.25 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 17 TYR 0.015 0.001 TYR A 144 PHE 0.014 0.001 PHE A 347 TRP 0.012 0.001 TRP A 198 HIS 0.004 0.001 HIS A 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.16 ( 7032) covalent geometry : angle 0.53034 / 0.27 ( 9584) hydrogen bonds : bond 0.04109 / 2.78 ( 278) hydrogen bonds : angle 5.08368 / 3.33 ( 744) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 155 time to evaluate : 0.193 Fit side-chains REVERT: A 273 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6937 (mp0) REVERT: B 67 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7712 (tm-30) REVERT: B 242 ASP cc_start: 0.7505 (m-30) cc_final: 0.7265 (m-30) REVERT: B 364 ASN cc_start: 0.8777 (m-40) cc_final: 0.8444 (m-40) REVERT: B 405 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7566 (tt0) outliers start: 15 outliers final: 7 residues processed: 161 average time/residue: 0.7682 time to fit residues: 128.0844 Evaluate side-chains 160 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 151 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 394 LYS Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 300 LYS Chi-restraints excluded: chain B residue 363 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 42 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 37 optimal weight: 0.3980 chunk 33 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 26 optimal weight: 0.3980 chunk 6 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 343 GLN A 428 GLN B 343 GLN B 369 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.110050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.100016 restraints weight = 8462.454| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.35 r_work: 0.3290 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 7032 Z= 0.208 Angle : 0.568 6.856 9584 Z= 0.292 Chirality : 0.049 0.137 1048 Planarity : 0.005 0.041 1260 Dihedral : 4.788 19.816 950 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.84 % Allowed : 14.86 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.29), residues: 862 helix: 1.77 (0.31), residues: 256 sheet: -0.26 (0.43), residues: 154 loop : 0.27 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 17 TYR 0.017 0.002 TYR A 144 PHE 0.011 0.001 PHE B 347 TRP 0.012 0.002 TRP B 194 HIS 0.005 0.001 HIS B 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.21 ( 7032) covalent geometry : angle 0.56847 / 0.29 ( 9584) hydrogen bonds : bond 0.04485 / 3.04 ( 278) hydrogen bonds : angle 5.14316 / 3.38 ( 744) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 150 time to evaluate : 0.188 Fit side-chains REVERT: A 113 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.7362 (mmt) REVERT: A 273 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.7016 (mp0) REVERT: B 67 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7667 (tm-30) REVERT: B 242 ASP cc_start: 0.7508 (m-30) cc_final: 0.7271 (m-30) REVERT: B 364 ASN cc_start: 0.8788 (m-40) cc_final: 0.8430 (m-40) REVERT: B 405 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7569 (tt0) outliers start: 21 outliers final: 11 residues processed: 157 average time/residue: 0.7471 time to fit residues: 121.4208 Evaluate side-chains 163 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 149 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 343 GLN Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 394 LYS Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 300 LYS Chi-restraints excluded: chain B residue 343 GLN Chi-restraints excluded: chain B residue 363 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 83 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 73 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 428 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.111063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.101100 restraints weight = 8440.398| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.34 r_work: 0.3309 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7032 Z= 0.147 Angle : 0.548 8.039 9584 Z= 0.280 Chirality : 0.047 0.137 1048 Planarity : 0.005 0.038 1260 Dihedral : 4.641 18.797 950 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.03 % Allowed : 16.22 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.29), residues: 862 helix: 1.89 (0.31), residues: 256 sheet: -0.21 (0.43), residues: 154 loop : 0.36 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 17 TYR 0.016 0.001 TYR A 144 PHE 0.012 0.001 PHE A 347 TRP 0.012 0.001 TRP B 198 HIS 0.003 0.001 HIS B 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 ( 7032) covalent geometry : angle 0.54801 / 0.28 ( 9584) hydrogen bonds : bond 0.04040 / 2.74 ( 278) hydrogen bonds : angle 5.03895 / 3.29 ( 744) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 152 time to evaluate : 0.238 Fit side-chains REVERT: A 273 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6982 (mp0) REVERT: B 67 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7627 (tm-30) REVERT: B 242 ASP cc_start: 0.7496 (m-30) cc_final: 0.7254 (m-30) REVERT: B 364 ASN cc_start: 0.8772 (m-40) cc_final: 0.8410 (m-40) REVERT: B 405 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7657 (tt0) outliers start: 15 outliers final: 8 residues processed: 156 average time/residue: 0.7755 time to fit residues: 125.3693 Evaluate side-chains 158 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 148 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 394 LYS Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 300 LYS Chi-restraints excluded: chain B residue 363 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 0 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 5 optimal weight: 0.0980 chunk 70 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 343 GLN A 428 GLN B 343 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.110465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.100431 restraints weight = 8453.026| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.35 r_work: 0.3297 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 7032 Z= 0.189 Angle : 0.572 6.805 9584 Z= 0.295 Chirality : 0.048 0.138 1048 Planarity : 0.005 0.041 1260 Dihedral : 4.754 19.479 950 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.16 % Allowed : 16.35 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.29), residues: 862 helix: 1.85 (0.31), residues: 256 sheet: -0.08 (0.43), residues: 144 loop : 0.35 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 17 TYR 0.016 0.002 TYR A 144 PHE 0.010 0.001 PHE B 347 TRP 0.013 0.002 TRP A 198 HIS 0.004 0.001 HIS B 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.19 ( 7032) covalent geometry : angle 0.57236 / 0.30 ( 9584) hydrogen bonds : bond 0.04341 / 2.94 ( 278) hydrogen bonds : angle 5.09967 / 3.34 ( 744) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 148 time to evaluate : 0.278 Fit side-chains REVERT: A 273 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.7052 (mp0) REVERT: B 67 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7662 (tm-30) REVERT: B 242 ASP cc_start: 0.7518 (m-30) cc_final: 0.7279 (m-30) REVERT: B 364 ASN cc_start: 0.8788 (m-40) cc_final: 0.8460 (m-40) REVERT: B 405 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7566 (tt0) outliers start: 16 outliers final: 9 residues processed: 154 average time/residue: 0.8109 time to fit residues: 129.3074 Evaluate side-chains 157 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 146 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 343 GLN Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 394 LYS Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 300 LYS Chi-restraints excluded: chain B residue 343 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 5 optimal weight: 0.3980 chunk 40 optimal weight: 3.9990 chunk 38 optimal weight: 0.0770 chunk 4 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 343 GLN A 428 GLN B 343 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.111610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.101567 restraints weight = 8424.509| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.35 r_work: 0.3316 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7032 Z= 0.128 Angle : 0.548 7.948 9584 Z= 0.281 Chirality : 0.046 0.140 1048 Planarity : 0.005 0.042 1260 Dihedral : 4.583 18.259 950 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.43 % Allowed : 15.68 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.29), residues: 862 helix: 2.05 (0.31), residues: 256 sheet: -0.13 (0.43), residues: 154 loop : 0.49 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 17 TYR 0.014 0.001 TYR A 144 PHE 0.012 0.001 PHE B 347 TRP 0.016 0.001 TRP A 198 HIS 0.002 0.001 HIS B 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 ( 7032) covalent geometry : angle 0.54803 / 0.28 ( 9584) hydrogen bonds : bond 0.03870 / 2.63 ( 278) hydrogen bonds : angle 4.98113 / 3.25 ( 744) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 152 time to evaluate : 0.192 Fit side-chains REVERT: A 273 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.7013 (mp0) REVERT: B 67 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7639 (tm-30) REVERT: B 242 ASP cc_start: 0.7508 (m-30) cc_final: 0.7264 (m-30) REVERT: B 364 ASN cc_start: 0.8786 (m-40) cc_final: 0.8431 (m-40) REVERT: B 405 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7641 (tt0) outliers start: 18 outliers final: 13 residues processed: 160 average time/residue: 0.7473 time to fit residues: 123.9002 Evaluate side-chains 166 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 151 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASP Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 343 GLN Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 394 LYS Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 300 LYS Chi-restraints excluded: chain B residue 312 ARG Chi-restraints excluded: chain B residue 343 GLN Chi-restraints excluded: chain B residue 363 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 6 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 80 optimal weight: 0.0770 chunk 54 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.7342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 343 GLN A 428 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.111372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.101270 restraints weight = 8383.150| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.35 r_work: 0.3309 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7032 Z= 0.152 Angle : 0.555 8.293 9584 Z= 0.284 Chirality : 0.047 0.137 1048 Planarity : 0.005 0.041 1260 Dihedral : 4.638 18.704 950 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.89 % Allowed : 16.35 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.29), residues: 862 helix: 2.01 (0.31), residues: 256 sheet: -0.15 (0.43), residues: 154 loop : 0.53 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 312 TYR 0.014 0.001 TYR A 144 PHE 0.013 0.001 PHE A 347 TRP 0.013 0.001 TRP A 198 HIS 0.003 0.001 HIS B 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.15 ( 7032) covalent geometry : angle 0.55540 / 0.28 ( 9584) hydrogen bonds : bond 0.04030 / 2.73 ( 278) hydrogen bonds : angle 4.96995 / 3.25 ( 744) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1724 Ramachandran restraints generated. 862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 152 time to evaluate : 0.163 Fit side-chains REVERT: B 242 ASP cc_start: 0.7509 (m-30) cc_final: 0.7266 (m-30) REVERT: B 364 ASN cc_start: 0.8791 (m-40) cc_final: 0.8445 (m-40) REVERT: B 405 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7599 (tt0) outliers start: 14 outliers final: 10 residues processed: 156 average time/residue: 0.7571 time to fit residues: 122.3886 Evaluate side-chains 162 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 152 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 300 LYS Chi-restraints excluded: chain A residue 343 GLN Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 394 LYS Chi-restraints excluded: chain B residue 78 ASP Chi-restraints excluded: chain B residue 264 ASP Chi-restraints excluded: chain B residue 300 LYS Chi-restraints excluded: chain B residue 312 ARG Chi-restraints excluded: chain B residue 363 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 0 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 85 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 343 GLN B 369 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.111302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.101160 restraints weight = 8436.030| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.37 r_work: 0.3306 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7032 Z= 0.166 Angle : 0.561 8.391 9584 Z= 0.288 Chirality : 0.047 0.138 1048 Planarity : 0.005 0.041 1260 Dihedral : 4.684 18.928 950 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.03 % Allowed : 17.16 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.29), residues: 862 helix: 2.00 (0.31), residues: 256 sheet: -0.17 (0.42), residues: 154 loop : 0.54 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 312 TYR 0.016 0.001 TYR A 187 PHE 0.013 0.001 PHE A 347 TRP 0.012 0.002 TRP A 198 HIS 0.004 0.001 HIS B 318 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.17 ( 7032) covalent geometry : angle 0.56095 / 0.29 ( 9584) hydrogen bonds : bond 0.04124 / 2.79 ( 278) hydrogen bonds : angle 4.99009 / 3.27 ( 744) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3203.43 seconds wall clock time: 55 minutes 8.17 seconds (3308.17 seconds total)