Starting phenix.real_space_refine on Sat Jul 26 21:11:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8trm_41583/07_2025/8trm_41583.cif Found real_map, /net/cci-nas-00/data/ceres_data/8trm_41583/07_2025/8trm_41583.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8trm_41583/07_2025/8trm_41583.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8trm_41583/07_2025/8trm_41583.map" model { file = "/net/cci-nas-00/data/ceres_data/8trm_41583/07_2025/8trm_41583.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8trm_41583/07_2025/8trm_41583.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.359 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 3 5.21 5 S 57 5.16 5 C 5544 2.51 5 N 1470 2.21 5 O 1734 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 8814 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 19, 'TRANS': 351} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Restraints were copied for chains: C, B Time building chain proxies: 6.03, per 1000 atoms: 0.68 Number of scatterers: 8814 At special positions: 0 Unit cell: (77.464, 99.356, 138.93, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 57 16.00 P 6 15.00 Mg 3 11.99 O 1734 8.00 N 1470 7.00 C 5544 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.91 Conformation dependent library (CDL) restraints added in 1.4 seconds 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2046 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 18 sheets defined 50.1% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.92 Creating SS restraints... Processing helix chain 'A' and resid 56 through 62 Processing helix chain 'A' and resid 79 through 93 Processing helix chain 'A' and resid 113 through 127 removed outlier: 4.018A pdb=" N ARG A 117 " --> pdb=" O PRO A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 146 Processing helix chain 'A' and resid 173 through 176 Processing helix chain 'A' and resid 182 through 194 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 203 through 218 Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 253 through 258 Processing helix chain 'A' and resid 259 through 263 Processing helix chain 'A' and resid 264 through 269 Processing helix chain 'A' and resid 274 through 285 Processing helix chain 'A' and resid 290 through 297 Processing helix chain 'A' and resid 302 through 306 removed outlier: 3.575A pdb=" N THR A 305 " --> pdb=" O GLY A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 322 Processing helix chain 'A' and resid 335 through 337 No H-bonds generated for 'chain 'A' and resid 335 through 337' Processing helix chain 'A' and resid 338 through 349 Processing helix chain 'A' and resid 350 through 356 removed outlier: 3.540A pdb=" N GLN A 354 " --> pdb=" O SER A 351 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLN A 355 " --> pdb=" O THR A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 367 Processing helix chain 'A' and resid 369 through 375 removed outlier: 4.113A pdb=" N ARG A 373 " --> pdb=" O SER A 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 62 Processing helix chain 'B' and resid 79 through 93 Processing helix chain 'B' and resid 113 through 127 removed outlier: 4.019A pdb=" N ARG B 117 " --> pdb=" O PRO B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 146 Processing helix chain 'B' and resid 173 through 176 Processing helix chain 'B' and resid 182 through 194 Processing helix chain 'B' and resid 195 through 198 Processing helix chain 'B' and resid 203 through 218 Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 253 through 258 Processing helix chain 'B' and resid 259 through 263 Processing helix chain 'B' and resid 264 through 269 Processing helix chain 'B' and resid 274 through 285 Processing helix chain 'B' and resid 290 through 297 Processing helix chain 'B' and resid 302 through 306 removed outlier: 3.575A pdb=" N THR B 305 " --> pdb=" O GLY B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 322 Processing helix chain 'B' and resid 335 through 337 No H-bonds generated for 'chain 'B' and resid 335 through 337' Processing helix chain 'B' and resid 338 through 349 Processing helix chain 'B' and resid 350 through 356 removed outlier: 3.540A pdb=" N GLN B 354 " --> pdb=" O SER B 351 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLN B 355 " --> pdb=" O THR B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 367 Processing helix chain 'B' and resid 369 through 375 removed outlier: 4.113A pdb=" N ARG B 373 " --> pdb=" O SER B 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 62 Processing helix chain 'C' and resid 79 through 93 Processing helix chain 'C' and resid 113 through 127 removed outlier: 4.018A pdb=" N ARG C 117 " --> pdb=" O PRO C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 146 Processing helix chain 'C' and resid 173 through 176 Processing helix chain 'C' and resid 182 through 194 Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 203 through 218 Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 253 through 258 Processing helix chain 'C' and resid 259 through 263 Processing helix chain 'C' and resid 264 through 269 Processing helix chain 'C' and resid 274 through 285 Processing helix chain 'C' and resid 290 through 297 Processing helix chain 'C' and resid 302 through 306 removed outlier: 3.574A pdb=" N THR C 305 " --> pdb=" O GLY C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 322 Processing helix chain 'C' and resid 335 through 337 No H-bonds generated for 'chain 'C' and resid 335 through 337' Processing helix chain 'C' and resid 338 through 349 Processing helix chain 'C' and resid 350 through 356 removed outlier: 3.540A pdb=" N GLN C 354 " --> pdb=" O SER C 351 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLN C 355 " --> pdb=" O THR C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 367 Processing helix chain 'C' and resid 369 through 375 removed outlier: 4.113A pdb=" N ARG C 373 " --> pdb=" O SER C 369 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 33 removed outlier: 6.669A pdb=" N LEU A 9 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N THR A 107 " --> pdb=" O LEU A 9 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N VAL A 11 " --> pdb=" O THR A 107 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 72 through 73 Processing sheet with id=AA4, first strand: chain 'A' and resid 170 through 171 Processing sheet with id=AA5, first strand: chain 'A' and resid 170 through 171 removed outlier: 6.832A pdb=" N VAL A 298 " --> pdb=" O VAL A 331 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 239 through 242 Processing sheet with id=AA7, first strand: chain 'B' and resid 30 through 33 removed outlier: 6.669A pdb=" N LEU B 9 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N THR B 107 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N VAL B 11 " --> pdb=" O THR B 107 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AA9, first strand: chain 'B' and resid 72 through 73 Processing sheet with id=AB1, first strand: chain 'B' and resid 170 through 171 Processing sheet with id=AB2, first strand: chain 'B' and resid 170 through 171 removed outlier: 6.832A pdb=" N VAL B 298 " --> pdb=" O VAL B 331 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 239 through 242 Processing sheet with id=AB4, first strand: chain 'C' and resid 30 through 33 removed outlier: 6.669A pdb=" N LEU C 9 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N THR C 107 " --> pdb=" O LEU C 9 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N VAL C 11 " --> pdb=" O THR C 107 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AB6, first strand: chain 'C' and resid 72 through 73 Processing sheet with id=AB7, first strand: chain 'C' and resid 170 through 171 Processing sheet with id=AB8, first strand: chain 'C' and resid 170 through 171 removed outlier: 6.832A pdb=" N VAL C 298 " --> pdb=" O VAL C 331 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 239 through 242 447 hydrogen bonds defined for protein. 1143 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: 3.88 Time building geometry restraints manager: 2.82 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: 2870 1.34 - 1.46: 1656 1.46 - 1.57: 4339 1.57 - 1.69: 9 1.69 - 1.81: 99 Bond restraints: 8973 Sorted by residual: bond pdb=" N ASP B 212 " pdb=" CA ASP B 212 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.19e-02 7.06e+03 4.76e+00 bond pdb=" N ASP C 212 " pdb=" CA ASP C 212 " ideal model delta sigma weight residual 1.459 1.485 -0.025 1.19e-02 7.06e+03 4.55e+00 bond pdb=" N ASP A 212 " pdb=" CA ASP A 212 " ideal model delta sigma weight residual 1.459 1.485 -0.025 1.19e-02 7.06e+03 4.50e+00 bond pdb=" C4 ADP C 402 " pdb=" C5 ADP C 402 " ideal model delta sigma weight residual 1.490 1.466 0.024 2.00e-02 2.50e+03 1.43e+00 bond pdb=" C4 ADP A 402 " pdb=" C5 ADP A 402 " ideal model delta sigma weight residual 1.490 1.466 0.024 2.00e-02 2.50e+03 1.43e+00 ... (remaining 8968 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 11802 1.41 - 2.82: 247 2.82 - 4.24: 86 4.24 - 5.65: 13 5.65 - 7.06: 14 Bond angle restraints: 12162 Sorted by residual: angle pdb=" N ILE C 290 " pdb=" CA ILE C 290 " pdb=" C ILE C 290 " ideal model delta sigma weight residual 113.42 109.06 4.36 1.17e+00 7.31e-01 1.39e+01 angle pdb=" N ILE B 290 " pdb=" CA ILE B 290 " pdb=" C ILE B 290 " ideal model delta sigma weight residual 113.42 109.06 4.36 1.17e+00 7.31e-01 1.39e+01 angle pdb=" N ILE A 290 " pdb=" CA ILE A 290 " pdb=" C ILE A 290 " ideal model delta sigma weight residual 113.42 109.07 4.35 1.17e+00 7.31e-01 1.38e+01 angle pdb=" CA ILE A 290 " pdb=" C ILE A 290 " pdb=" N ARG A 291 " ideal model delta sigma weight residual 118.90 115.55 3.35 9.40e-01 1.13e+00 1.27e+01 angle pdb=" CA ILE B 290 " pdb=" C ILE B 290 " pdb=" N ARG B 291 " ideal model delta sigma weight residual 118.90 115.58 3.32 9.40e-01 1.13e+00 1.25e+01 ... (remaining 12157 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.62: 5010 28.62 - 57.24: 351 57.24 - 85.86: 36 85.86 - 114.48: 3 114.48 - 143.10: 6 Dihedral angle restraints: 5406 sinusoidal: 2205 harmonic: 3201 Sorted by residual: dihedral pdb=" O1B ADP C 402 " pdb=" O3A ADP C 402 " pdb=" PB ADP C 402 " pdb=" PA ADP C 402 " ideal model delta sinusoidal sigma weight residual -60.00 83.10 -143.10 1 2.00e+01 2.50e-03 4.32e+01 dihedral pdb=" O1B ADP B 402 " pdb=" O3A ADP B 402 " pdb=" PB ADP B 402 " pdb=" PA ADP B 402 " ideal model delta sinusoidal sigma weight residual -60.00 83.07 -143.08 1 2.00e+01 2.50e-03 4.32e+01 dihedral pdb=" O1B ADP A 402 " pdb=" O3A ADP A 402 " pdb=" PB ADP A 402 " pdb=" PA ADP A 402 " ideal model delta sinusoidal sigma weight residual -60.00 83.05 -143.05 1 2.00e+01 2.50e-03 4.32e+01 ... (remaining 5403 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 654 0.027 - 0.053: 378 0.053 - 0.080: 156 0.080 - 0.106: 122 0.106 - 0.133: 34 Chirality restraints: 1344 Sorted by residual: chirality pdb=" CA ILE A 358 " pdb=" N ILE A 358 " pdb=" C ILE A 358 " pdb=" CB ILE A 358 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.41e-01 chirality pdb=" CA ILE B 358 " pdb=" N ILE B 358 " pdb=" C ILE B 358 " pdb=" CB ILE B 358 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA ILE C 358 " pdb=" N ILE C 358 " pdb=" C ILE C 358 " pdb=" CB ILE C 358 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.26e-01 ... (remaining 1341 not shown) Planarity restraints: 1557 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 164 " 0.021 5.00e-02 4.00e+02 3.13e-02 1.57e+00 pdb=" N PRO A 165 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 165 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 165 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 164 " -0.020 5.00e-02 4.00e+02 3.11e-02 1.54e+00 pdb=" N PRO B 165 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO B 165 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 165 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 164 " -0.020 5.00e-02 4.00e+02 3.09e-02 1.53e+00 pdb=" N PRO C 165 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO C 165 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 165 " -0.017 5.00e-02 4.00e+02 ... (remaining 1554 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 42 2.51 - 3.11: 5956 3.11 - 3.70: 13252 3.70 - 4.30: 20131 4.30 - 4.90: 32954 Nonbonded interactions: 72335 Sorted by model distance: nonbonded pdb="MG MG A 401 " pdb=" O HOH A 507 " model vdw 1.909 2.170 nonbonded pdb="MG MG B 401 " pdb=" O HOH B 507 " model vdw 1.909 2.170 nonbonded pdb="MG MG C 401 " pdb=" O HOH C 507 " model vdw 1.909 2.170 nonbonded pdb="MG MG A 401 " pdb=" O HOH A 503 " model vdw 1.921 2.170 nonbonded pdb="MG MG C 401 " pdb=" O HOH C 503 " model vdw 1.921 2.170 ... (remaining 72330 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' 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: 35.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 28.170 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:17.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8949 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 : 0.003 0.029 8973 Z= 0.140 Angle : 0.606 7.058 12162 Z= 0.310 Chirality : 0.047 0.133 1344 Planarity : 0.004 0.031 1557 Dihedral : 18.288 143.104 3360 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.68 % Allowed : 15.67 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.26), residues: 1107 helix: 0.82 (0.25), residues: 459 sheet: 0.95 (0.37), residues: 186 loop : 1.55 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 80 HIS 0.003 0.001 HIS A 102 PHE 0.007 0.001 PHE C 256 TYR 0.009 0.001 TYR A 295 ARG 0.001 0.000 ARG A 257 Details of bonding type rmsd hydrogen bonds : bond 0.16277 ( 441) hydrogen bonds : angle 5.70776 ( 1143) covalent geometry : bond 0.00311 ( 8973) covalent geometry : angle 0.60590 (12162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 201 time to evaluate : 1.042 Fit side-chains REVERT: A 177 MET cc_start: 0.9077 (OUTLIER) cc_final: 0.8825 (mtm) REVERT: B 96 ARG cc_start: 0.8115 (mtp85) cc_final: 0.7906 (mtm-85) REVERT: B 168 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8460 (mm-30) REVERT: B 180 ASP cc_start: 0.8056 (OUTLIER) cc_final: 0.7709 (t0) REVERT: B 226 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7429 (mt-10) REVERT: B 229 LYS cc_start: 0.7756 (mtpm) cc_final: 0.7488 (mttm) REVERT: B 287 ASP cc_start: 0.8178 (m-30) cc_final: 0.7974 (m-30) REVERT: B 293 ASP cc_start: 0.8327 (m-30) cc_final: 0.8011 (m-30) REVERT: B 312 GLU cc_start: 0.8495 (mp0) cc_final: 0.8280 (mp0) REVERT: B 329 LYS cc_start: 0.8842 (tmtm) cc_final: 0.8624 (tptp) REVERT: B 354 GLN cc_start: 0.8499 (mm-40) cc_final: 0.8287 (mm-40) REVERT: B 362 GLU cc_start: 0.8475 (mt-10) cc_final: 0.7952 (mt-10) REVERT: C 51 LYS cc_start: 0.7915 (mtmt) cc_final: 0.7681 (mtpt) REVERT: C 84 GLU cc_start: 0.8460 (tt0) cc_final: 0.8251 (tt0) REVERT: C 96 ARG cc_start: 0.7868 (mtp85) cc_final: 0.7640 (mtt-85) REVERT: C 100 GLU cc_start: 0.8090 (pm20) cc_final: 0.7888 (pm20) REVERT: C 122 GLN cc_start: 0.8699 (tt0) cc_final: 0.8487 (tt0) REVERT: C 148 ARG cc_start: 0.8199 (mmm-85) cc_final: 0.7969 (mmt90) REVERT: C 168 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8392 (mt-10) REVERT: C 223 ASP cc_start: 0.8301 (t0) cc_final: 0.7973 (t0) REVERT: C 325 THR cc_start: 0.8732 (m) cc_final: 0.8382 (p) REVERT: C 355 GLN cc_start: 0.8178 (mm110) cc_final: 0.7872 (mp-120) outliers start: 16 outliers final: 4 residues processed: 208 average time/residue: 1.8050 time to fit residues: 393.7626 Evaluate side-chains 187 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 181 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain C residue 180 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.3108 r_free = 0.3108 target = 0.104098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.089745 restraints weight = 9998.713| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 1.34 r_work: 0.2790 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8979 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8973 Z= 0.175 Angle : 0.633 7.980 12162 Z= 0.317 Chirality : 0.048 0.163 1344 Planarity : 0.005 0.045 1557 Dihedral : 11.727 149.966 1249 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.89 % Allowed : 14.51 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.26), residues: 1107 helix: 0.97 (0.25), residues: 462 sheet: 0.92 (0.37), residues: 186 loop : 1.60 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP C 341 HIS 0.005 0.001 HIS B 162 PHE 0.011 0.001 PHE B 263 TYR 0.013 0.001 TYR C 295 ARG 0.003 0.000 ARG C 291 Details of bonding type rmsd hydrogen bonds : bond 0.05381 ( 441) hydrogen bonds : angle 4.80912 ( 1143) covalent geometry : bond 0.00419 ( 8973) covalent geometry : angle 0.63307 (12162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 186 time to evaluate : 0.980 Fit side-chains REVERT: A 96 ARG cc_start: 0.8313 (mtp85) cc_final: 0.7997 (mtm-85) REVERT: A 216 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8304 (mppt) REVERT: A 329 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8351 (tttm) REVERT: B 29 ARG cc_start: 0.8948 (OUTLIER) cc_final: 0.7985 (ptp-170) REVERT: B 58 GLU cc_start: 0.8406 (tt0) cc_final: 0.8149 (tt0) REVERT: B 73 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7320 (mp0) REVERT: B 229 LYS cc_start: 0.8011 (mtpm) cc_final: 0.7729 (mttm) REVERT: B 354 GLN cc_start: 0.8719 (mm-40) cc_final: 0.8475 (mm-40) REVERT: B 362 GLU cc_start: 0.8425 (mt-10) cc_final: 0.7927 (mt-10) REVERT: C 73 GLU cc_start: 0.8049 (mp0) cc_final: 0.7846 (mp0) REVERT: C 84 GLU cc_start: 0.8574 (tt0) cc_final: 0.8346 (tt0) REVERT: C 96 ARG cc_start: 0.8135 (mtp85) cc_final: 0.7918 (mtt-85) REVERT: C 122 GLN cc_start: 0.8868 (tt0) cc_final: 0.8649 (tt0) REVERT: C 168 GLU cc_start: 0.8729 (mm-30) cc_final: 0.8522 (mt-10) REVERT: C 223 ASP cc_start: 0.8376 (t0) cc_final: 0.7956 (t0) REVERT: C 325 THR cc_start: 0.8666 (m) cc_final: 0.8383 (p) REVERT: C 355 GLN cc_start: 0.8289 (mm110) cc_final: 0.8008 (mp-120) outliers start: 37 outliers final: 15 residues processed: 204 average time/residue: 1.5994 time to fit residues: 341.7613 Evaluate side-chains 196 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 177 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 329 LYS Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 292 LYS Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 292 LYS Chi-restraints excluded: chain C residue 352 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 32 optimal weight: 0.0170 chunk 24 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 2 optimal weight: 0.0870 chunk 93 optimal weight: 0.1980 chunk 10 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 62 optimal weight: 0.3980 overall best weight: 0.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.113746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.100412 restraints weight = 10462.492| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 1.30 r_work: 0.2921 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8973 Z= 0.090 Angle : 0.543 6.573 12162 Z= 0.262 Chirality : 0.044 0.153 1344 Planarity : 0.004 0.032 1557 Dihedral : 11.060 156.453 1240 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.52 % Allowed : 16.61 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.26), residues: 1107 helix: 1.31 (0.25), residues: 462 sheet: 0.95 (0.36), residues: 201 loop : 1.88 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 80 HIS 0.002 0.001 HIS A 162 PHE 0.006 0.001 PHE B 256 TYR 0.010 0.001 TYR A 295 ARG 0.005 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.03366 ( 441) hydrogen bonds : angle 4.53519 ( 1143) covalent geometry : bond 0.00191 ( 8973) covalent geometry : angle 0.54260 (12162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 195 time to evaluate : 1.092 Fit side-chains REVERT: A 329 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8348 (tttm) REVERT: A 360 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.7787 (tptm) REVERT: B 29 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.8004 (ptp-170) REVERT: B 58 GLU cc_start: 0.8253 (tt0) cc_final: 0.8010 (tt0) REVERT: B 96 ARG cc_start: 0.8308 (mtt-85) cc_final: 0.7960 (mtm-85) REVERT: B 229 LYS cc_start: 0.7999 (mtpm) cc_final: 0.7721 (mttp) REVERT: B 293 ASP cc_start: 0.8350 (m-30) cc_final: 0.8056 (m-30) REVERT: B 335 GLU cc_start: 0.8437 (pm20) cc_final: 0.8155 (pm20) REVERT: B 354 GLN cc_start: 0.8572 (mm-40) cc_final: 0.8338 (mm-40) REVERT: B 362 GLU cc_start: 0.8390 (mt-10) cc_final: 0.7855 (mt-10) REVERT: C 84 GLU cc_start: 0.8496 (tt0) cc_final: 0.8212 (mt-10) REVERT: C 96 ARG cc_start: 0.8140 (mtp85) cc_final: 0.7899 (mtt-85) REVERT: C 168 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8441 (mt-10) REVERT: C 212 ASP cc_start: 0.8751 (t70) cc_final: 0.8520 (t70) REVERT: C 223 ASP cc_start: 0.8277 (t0) cc_final: 0.7860 (t0) REVERT: C 325 THR cc_start: 0.8542 (m) cc_final: 0.8270 (p) REVERT: C 355 GLN cc_start: 0.8272 (mm110) cc_final: 0.7969 (mp-120) outliers start: 24 outliers final: 10 residues processed: 203 average time/residue: 1.5813 time to fit residues: 336.6644 Evaluate side-chains 194 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 181 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 329 LYS Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 360 LYS Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 29 ARG Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 237 ILE Chi-restraints excluded: chain B residue 292 LYS Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 366 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 19 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- 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 = 0.3160 r_free = 0.3160 target = 0.107233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.093557 restraints weight = 10127.614| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 1.28 r_work: 0.2805 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9003 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 8973 Z= 0.252 Angle : 0.685 8.164 12162 Z= 0.344 Chirality : 0.052 0.172 1344 Planarity : 0.005 0.045 1557 Dihedral : 11.733 155.915 1239 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.58 % Allowed : 15.56 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.25), residues: 1107 helix: 1.06 (0.25), residues: 459 sheet: 0.75 (0.35), residues: 207 loop : 1.62 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP A 341 HIS 0.006 0.002 HIS B 162 PHE 0.013 0.002 PHE B 263 TYR 0.012 0.002 TYR C 241 ARG 0.004 0.001 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.06053 ( 441) hydrogen bonds : angle 4.81075 ( 1143) covalent geometry : bond 0.00625 ( 8973) covalent geometry : angle 0.68513 (12162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 186 time to evaluate : 1.005 Fit side-chains REVERT: A 65 ILE cc_start: 0.9403 (OUTLIER) cc_final: 0.8814 (pp) REVERT: A 73 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7359 (mp0) REVERT: A 223 ASP cc_start: 0.8463 (t0) cc_final: 0.8255 (t0) REVERT: A 329 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8335 (tttm) REVERT: B 58 GLU cc_start: 0.8412 (tt0) cc_final: 0.8187 (tt0) REVERT: B 73 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7473 (mp0) REVERT: B 177 MET cc_start: 0.9216 (mmm) cc_final: 0.8799 (mtp) REVERT: B 229 LYS cc_start: 0.8095 (mtpm) cc_final: 0.7783 (mttt) REVERT: B 308 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8007 (tm-30) REVERT: B 335 GLU cc_start: 0.8501 (pm20) cc_final: 0.8286 (pm20) REVERT: B 354 GLN cc_start: 0.8766 (mm-40) cc_final: 0.8492 (mm-40) REVERT: B 362 GLU cc_start: 0.8453 (mt-10) cc_final: 0.7934 (mt-10) REVERT: C 84 GLU cc_start: 0.8585 (tt0) cc_final: 0.8360 (tt0) REVERT: C 168 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8554 (mt-10) REVERT: C 212 ASP cc_start: 0.8768 (t70) cc_final: 0.8492 (t70) REVERT: C 223 ASP cc_start: 0.8455 (t0) cc_final: 0.8036 (t0) REVERT: C 325 THR cc_start: 0.8672 (m) cc_final: 0.8459 (p) REVERT: C 373 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7738 (ptm-80) outliers start: 34 outliers final: 13 residues processed: 203 average time/residue: 1.5288 time to fit residues: 326.6753 Evaluate side-chains 196 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 177 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 329 LYS Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 292 LYS Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 366 SER Chi-restraints excluded: chain C residue 373 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 45 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 107 optimal weight: 3.9990 chunk 73 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 76 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 ASN C 122 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.111128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.097638 restraints weight = 10291.840| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 1.28 r_work: 0.2856 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8943 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8973 Z= 0.113 Angle : 0.570 7.135 12162 Z= 0.278 Chirality : 0.045 0.163 1344 Planarity : 0.004 0.035 1557 Dihedral : 11.351 160.185 1239 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.63 % Allowed : 17.03 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.26), residues: 1107 helix: 1.24 (0.25), residues: 462 sheet: 1.02 (0.36), residues: 198 loop : 1.68 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 80 HIS 0.003 0.001 HIS A 162 PHE 0.008 0.001 PHE B 256 TYR 0.010 0.001 TYR B 295 ARG 0.006 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.03937 ( 441) hydrogen bonds : angle 4.56792 ( 1143) covalent geometry : bond 0.00256 ( 8973) covalent geometry : angle 0.57019 (12162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 189 time to evaluate : 0.955 Fit side-chains REVERT: A 329 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8352 (tttm) REVERT: A 360 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.7793 (tptm) REVERT: B 58 GLU cc_start: 0.8290 (tt0) cc_final: 0.8080 (tt0) REVERT: B 73 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7441 (mp0) REVERT: B 177 MET cc_start: 0.9135 (mmm) cc_final: 0.8518 (mtp) REVERT: B 229 LYS cc_start: 0.8041 (mtpm) cc_final: 0.7738 (mttt) REVERT: B 293 ASP cc_start: 0.8282 (m-30) cc_final: 0.7976 (m-30) REVERT: B 335 GLU cc_start: 0.8478 (pm20) cc_final: 0.8227 (pm20) REVERT: B 354 GLN cc_start: 0.8636 (mm-40) cc_final: 0.8385 (mm-40) REVERT: B 362 GLU cc_start: 0.8442 (mt-10) cc_final: 0.7887 (mt-10) REVERT: C 41 ASN cc_start: 0.8168 (m110) cc_final: 0.7917 (m110) REVERT: C 84 GLU cc_start: 0.8541 (tt0) cc_final: 0.8312 (tt0) REVERT: C 168 GLU cc_start: 0.8727 (mm-30) cc_final: 0.8486 (mt-10) REVERT: C 212 ASP cc_start: 0.8772 (t70) cc_final: 0.8505 (t70) REVERT: C 223 ASP cc_start: 0.8336 (t0) cc_final: 0.7934 (t0) REVERT: C 325 THR cc_start: 0.8600 (m) cc_final: 0.8386 (p) REVERT: C 355 GLN cc_start: 0.8307 (mm110) cc_final: 0.7977 (mp-120) outliers start: 25 outliers final: 14 residues processed: 196 average time/residue: 1.6126 time to fit residues: 331.4753 Evaluate side-chains 200 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 183 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 329 LYS Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 360 LYS Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 292 LYS Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 366 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 34 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 36 optimal weight: 0.1980 chunk 2 optimal weight: 0.5980 chunk 23 optimal weight: 0.4980 chunk 85 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3215 r_free = 0.3215 target = 0.111275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.097844 restraints weight = 10300.027| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 1.28 r_work: 0.2880 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8942 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8973 Z= 0.114 Angle : 0.575 7.023 12162 Z= 0.279 Chirality : 0.045 0.160 1344 Planarity : 0.004 0.040 1557 Dihedral : 11.276 162.649 1239 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.73 % Allowed : 16.82 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.26), residues: 1107 helix: 1.31 (0.25), residues: 462 sheet: 1.03 (0.36), residues: 198 loop : 1.70 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 80 HIS 0.003 0.001 HIS A 162 PHE 0.009 0.001 PHE B 256 TYR 0.009 0.001 TYR B 295 ARG 0.009 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.03912 ( 441) hydrogen bonds : angle 4.51356 ( 1143) covalent geometry : bond 0.00261 ( 8973) covalent geometry : angle 0.57493 (12162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 187 time to evaluate : 1.091 Fit side-chains REVERT: A 65 ILE cc_start: 0.9394 (OUTLIER) cc_final: 0.8770 (pp) REVERT: A 73 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7320 (mp0) REVERT: A 216 LYS cc_start: 0.8695 (mptp) cc_final: 0.8399 (tppt) REVERT: A 329 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8357 (tttm) REVERT: A 360 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.7803 (tptm) REVERT: B 58 GLU cc_start: 0.8288 (tt0) cc_final: 0.8071 (tt0) REVERT: B 73 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7441 (mp0) REVERT: B 229 LYS cc_start: 0.8036 (mtpm) cc_final: 0.7748 (mttt) REVERT: B 293 ASP cc_start: 0.8319 (m-30) cc_final: 0.7988 (m-30) REVERT: B 335 GLU cc_start: 0.8466 (pm20) cc_final: 0.8227 (pm20) REVERT: B 362 GLU cc_start: 0.8451 (mt-10) cc_final: 0.7941 (mt-10) REVERT: C 41 ASN cc_start: 0.8158 (m110) cc_final: 0.7925 (m110) REVERT: C 84 GLU cc_start: 0.8538 (tt0) cc_final: 0.8308 (tt0) REVERT: C 168 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8466 (mt-10) REVERT: C 212 ASP cc_start: 0.8768 (t70) cc_final: 0.8507 (t70) REVERT: C 223 ASP cc_start: 0.8347 (t0) cc_final: 0.7955 (t0) REVERT: C 229 LYS cc_start: 0.8242 (mtpp) cc_final: 0.7861 (mtmt) REVERT: C 325 THR cc_start: 0.8595 (m) cc_final: 0.8375 (p) REVERT: C 355 GLN cc_start: 0.8309 (mm110) cc_final: 0.7988 (mp-120) outliers start: 26 outliers final: 13 residues processed: 197 average time/residue: 1.5765 time to fit residues: 326.8687 Evaluate side-chains 201 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 183 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 329 LYS Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 360 LYS Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 292 LYS Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 366 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 26 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 99 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 = 0.3174 r_free = 0.3174 target = 0.108392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.094819 restraints weight = 10304.739| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 1.28 r_work: 0.2807 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8979 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8973 Z= 0.190 Angle : 0.642 7.716 12162 Z= 0.318 Chirality : 0.049 0.171 1344 Planarity : 0.005 0.043 1557 Dihedral : 11.564 162.059 1239 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.36 % Allowed : 16.09 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.26), residues: 1107 helix: 1.11 (0.25), residues: 462 sheet: 0.86 (0.36), residues: 201 loop : 1.67 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP A 341 HIS 0.004 0.001 HIS A 102 PHE 0.011 0.002 PHE B 256 TYR 0.009 0.001 TYR C 295 ARG 0.009 0.001 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.05207 ( 441) hydrogen bonds : angle 4.68803 ( 1143) covalent geometry : bond 0.00462 ( 8973) covalent geometry : angle 0.64173 (12162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 178 time to evaluate : 0.982 Fit side-chains REVERT: A 65 ILE cc_start: 0.9417 (OUTLIER) cc_final: 0.8817 (pp) REVERT: A 216 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8425 (mppt) REVERT: A 329 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8350 (tttm) REVERT: A 360 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.7737 (tptm) REVERT: B 58 GLU cc_start: 0.8343 (tt0) cc_final: 0.8126 (tt0) REVERT: B 73 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7463 (mp0) REVERT: B 228 MET cc_start: 0.8810 (mmm) cc_final: 0.8594 (mmm) REVERT: B 229 LYS cc_start: 0.8082 (mtpm) cc_final: 0.7771 (mttt) REVERT: B 335 GLU cc_start: 0.8504 (pm20) cc_final: 0.8295 (pm20) REVERT: B 354 GLN cc_start: 0.8731 (mm-40) cc_final: 0.8378 (mm-40) REVERT: B 362 GLU cc_start: 0.8450 (mt-10) cc_final: 0.7909 (mt-10) REVERT: C 84 GLU cc_start: 0.8574 (tt0) cc_final: 0.8356 (tt0) REVERT: C 168 GLU cc_start: 0.8764 (mm-30) cc_final: 0.8517 (mt-10) REVERT: C 212 ASP cc_start: 0.8771 (t70) cc_final: 0.8488 (t70) REVERT: C 223 ASP cc_start: 0.8414 (t0) cc_final: 0.7969 (t0) REVERT: C 325 THR cc_start: 0.8684 (m) cc_final: 0.8476 (p) outliers start: 32 outliers final: 18 residues processed: 190 average time/residue: 1.7707 time to fit residues: 353.2066 Evaluate side-chains 203 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 180 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 329 LYS Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 360 LYS Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 292 LYS Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 366 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 36 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 4 optimal weight: 0.0870 chunk 56 optimal weight: 0.9980 chunk 81 optimal weight: 0.4980 chunk 67 optimal weight: 1.9990 chunk 76 optimal weight: 0.0970 chunk 5 optimal weight: 0.4980 overall best weight: 0.4356 ------------------------------------------------------------------------------- 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 = 0.3235 r_free = 0.3235 target = 0.112743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.099370 restraints weight = 10472.248| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 1.29 r_work: 0.2894 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8973 Z= 0.098 Angle : 0.562 7.627 12162 Z= 0.271 Chirality : 0.045 0.158 1344 Planarity : 0.004 0.039 1557 Dihedral : 11.201 166.389 1239 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.52 % Allowed : 17.35 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.26), residues: 1107 helix: 1.39 (0.25), residues: 462 sheet: 0.94 (0.37), residues: 201 loop : 1.75 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 80 HIS 0.003 0.001 HIS A 162 PHE 0.008 0.001 PHE B 256 TYR 0.009 0.001 TYR B 295 ARG 0.009 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.03456 ( 441) hydrogen bonds : angle 4.46915 ( 1143) covalent geometry : bond 0.00215 ( 8973) covalent geometry : angle 0.56192 (12162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 186 time to evaluate : 1.014 Fit side-chains REVERT: A 73 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7231 (mp0) REVERT: A 216 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8407 (tppt) REVERT: A 329 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8345 (tttm) REVERT: A 360 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.7787 (tptm) REVERT: B 58 GLU cc_start: 0.8269 (tt0) cc_final: 0.8035 (tt0) REVERT: B 73 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7436 (mp0) REVERT: B 229 LYS cc_start: 0.8024 (mtpm) cc_final: 0.7729 (mttt) REVERT: B 293 ASP cc_start: 0.8310 (m-30) cc_final: 0.7980 (m-30) REVERT: B 335 GLU cc_start: 0.8451 (pm20) cc_final: 0.8210 (pm20) REVERT: B 362 GLU cc_start: 0.8436 (mt-10) cc_final: 0.7908 (mt-10) REVERT: C 41 ASN cc_start: 0.8151 (m110) cc_final: 0.7916 (m110) REVERT: C 84 GLU cc_start: 0.8551 (tt0) cc_final: 0.8241 (mt-10) REVERT: C 168 GLU cc_start: 0.8678 (mm-30) cc_final: 0.8440 (mt-10) REVERT: C 212 ASP cc_start: 0.8770 (t70) cc_final: 0.8494 (t70) REVERT: C 223 ASP cc_start: 0.8326 (t0) cc_final: 0.7918 (t0) REVERT: C 229 LYS cc_start: 0.8221 (mtpp) cc_final: 0.7863 (mtmt) REVERT: C 355 GLN cc_start: 0.8302 (mm110) cc_final: 0.7980 (mp-120) outliers start: 24 outliers final: 12 residues processed: 195 average time/residue: 1.5772 time to fit residues: 323.0768 Evaluate side-chains 197 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 180 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 329 LYS Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 360 LYS Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 292 LYS Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 366 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 60 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 73 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 = 0.3183 r_free = 0.3183 target = 0.109109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.095608 restraints weight = 10288.024| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 1.27 r_work: 0.2841 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8975 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8973 Z= 0.170 Angle : 0.628 8.087 12162 Z= 0.310 Chirality : 0.048 0.162 1344 Planarity : 0.005 0.042 1557 Dihedral : 11.491 164.717 1239 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.42 % Allowed : 17.77 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.26), residues: 1107 helix: 1.19 (0.25), residues: 462 sheet: 0.88 (0.36), residues: 201 loop : 1.71 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP A 341 HIS 0.004 0.001 HIS A 102 PHE 0.010 0.001 PHE B 256 TYR 0.008 0.001 TYR C 295 ARG 0.009 0.001 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.04860 ( 441) hydrogen bonds : angle 4.61569 ( 1143) covalent geometry : bond 0.00413 ( 8973) covalent geometry : angle 0.62839 (12162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 177 time to evaluate : 1.085 Fit side-chains REVERT: A 65 ILE cc_start: 0.9413 (OUTLIER) cc_final: 0.8780 (pp) REVERT: A 73 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7287 (mp0) REVERT: A 216 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8415 (mppt) REVERT: A 329 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8365 (tttm) REVERT: A 360 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.7767 (tptm) REVERT: B 58 GLU cc_start: 0.8343 (tt0) cc_final: 0.8130 (tt0) REVERT: B 73 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7468 (mp0) REVERT: B 229 LYS cc_start: 0.8111 (mtpm) cc_final: 0.7811 (mttt) REVERT: B 335 GLU cc_start: 0.8500 (pm20) cc_final: 0.8286 (pm20) REVERT: B 362 GLU cc_start: 0.8438 (mt-10) cc_final: 0.7892 (mt-10) REVERT: C 84 GLU cc_start: 0.8576 (tt0) cc_final: 0.8355 (tt0) REVERT: C 168 GLU cc_start: 0.8743 (mm-30) cc_final: 0.8500 (mt-10) REVERT: C 212 ASP cc_start: 0.8770 (t70) cc_final: 0.8491 (t70) REVERT: C 223 ASP cc_start: 0.8415 (t0) cc_final: 0.8011 (t0) REVERT: C 229 LYS cc_start: 0.8296 (mtpp) cc_final: 0.7926 (mtmt) outliers start: 23 outliers final: 16 residues processed: 185 average time/residue: 1.6040 time to fit residues: 311.1742 Evaluate side-chains 198 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 176 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 329 LYS Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 360 LYS Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 65 ILE Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 292 LYS Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 366 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 59 optimal weight: 0.6980 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 68 optimal weight: 0.3980 chunk 29 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 7 optimal weight: 0.2980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3228 r_free = 0.3228 target = 0.112347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.098967 restraints weight = 10394.943| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 1.28 r_work: 0.2904 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8973 Z= 0.105 Angle : 0.577 8.550 12162 Z= 0.278 Chirality : 0.045 0.160 1344 Planarity : 0.004 0.042 1557 Dihedral : 11.192 168.205 1239 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.21 % Allowed : 17.98 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.26), residues: 1107 helix: 1.40 (0.25), residues: 462 sheet: 0.93 (0.37), residues: 201 loop : 1.75 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 80 HIS 0.003 0.001 HIS A 162 PHE 0.008 0.001 PHE B 256 TYR 0.009 0.001 TYR B 295 ARG 0.010 0.000 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.03611 ( 441) hydrogen bonds : angle 4.46551 ( 1143) covalent geometry : bond 0.00235 ( 8973) covalent geometry : angle 0.57703 (12162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 185 time to evaluate : 1.036 Fit side-chains REVERT: A 65 ILE cc_start: 0.9386 (OUTLIER) cc_final: 0.8748 (pp) REVERT: A 216 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8396 (mppt) REVERT: A 329 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8376 (tttm) REVERT: A 360 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.7791 (tptm) REVERT: B 58 GLU cc_start: 0.8279 (tt0) cc_final: 0.8050 (tt0) REVERT: B 73 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7457 (mp0) REVERT: B 229 LYS cc_start: 0.8024 (mtpm) cc_final: 0.7734 (mttt) REVERT: B 277 ARG cc_start: 0.8807 (mmt180) cc_final: 0.8599 (tpt170) REVERT: B 293 ASP cc_start: 0.8291 (m-30) cc_final: 0.7967 (m-30) REVERT: B 335 GLU cc_start: 0.8462 (pm20) cc_final: 0.8194 (pm20) REVERT: B 362 GLU cc_start: 0.8440 (mt-10) cc_final: 0.7925 (mt-10) REVERT: C 41 ASN cc_start: 0.8147 (m110) cc_final: 0.7918 (m110) REVERT: C 84 GLU cc_start: 0.8554 (tt0) cc_final: 0.8269 (mt-10) REVERT: C 168 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8454 (mt-10) REVERT: C 212 ASP cc_start: 0.8781 (t70) cc_final: 0.8520 (t70) REVERT: C 223 ASP cc_start: 0.8346 (t0) cc_final: 0.7948 (t0) REVERT: C 229 LYS cc_start: 0.8261 (mtpp) cc_final: 0.7890 (mtmt) REVERT: C 355 GLN cc_start: 0.8292 (mm110) cc_final: 0.7980 (mp-120) outliers start: 21 outliers final: 12 residues processed: 193 average time/residue: 1.5664 time to fit residues: 317.5079 Evaluate side-chains 200 residues out of total 951 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 183 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 329 LYS Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 360 LYS Chi-restraints excluded: chain B residue 7 GLN Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 292 LYS Chi-restraints excluded: chain B residue 352 THR Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 366 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 80 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.3174 r_free = 0.3174 target = 0.108409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.094806 restraints weight = 10420.479| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 1.29 r_work: 0.2813 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8984 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8973 Z= 0.194 Angle : 0.653 8.901 12162 Z= 0.323 Chirality : 0.049 0.167 1344 Planarity : 0.005 0.043 1557 Dihedral : 11.552 163.900 1239 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.42 % Allowed : 17.77 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.26), residues: 1107 helix: 1.13 (0.25), residues: 462 sheet: 0.87 (0.36), residues: 201 loop : 1.67 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP A 341 HIS 0.005 0.001 HIS A 102 PHE 0.011 0.002 PHE C 256 TYR 0.009 0.001 TYR C 241 ARG 0.009 0.001 ARG B 96 Details of bonding type rmsd hydrogen bonds : bond 0.05212 ( 441) hydrogen bonds : angle 4.66241 ( 1143) covalent geometry : bond 0.00473 ( 8973) covalent geometry : angle 0.65260 (12162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9533.43 seconds wall clock time: 165 minutes 47.65 seconds (9947.65 seconds total)