Starting phenix.real_space_refine on Fri Aug 22 20:29:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8isy_35700/08_2025/8isy_35700.cif Found real_map, /net/cci-nas-00/data/ceres_data/8isy_35700/08_2025/8isy_35700.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8isy_35700/08_2025/8isy_35700.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8isy_35700/08_2025/8isy_35700.map" model { file = "/net/cci-nas-00/data/ceres_data/8isy_35700/08_2025/8isy_35700.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8isy_35700/08_2025/8isy_35700.cif" } resolution = 3.27 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= -0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 23 5.16 5 C 5096 2.51 5 N 1308 2.21 5 O 1450 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7877 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 4117 Classifications: {'peptide': 507} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 478} Chain: "B" Number of atoms: 3760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3760 Classifications: {'peptide': 450} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 435} Time building chain proxies: 1.86, per 1000 atoms: 0.24 Number of scatterers: 7877 At special positions: 0 Unit cell: (82.82, 104.14, 117.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 23 16.00 O 1450 8.00 N 1308 7.00 C 5096 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: 0.62 Conformation dependent library (CDL) restraints added in 419.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1826 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 10 sheets defined 42.9% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 15 through 17 No H-bonds generated for 'chain 'A' and resid 15 through 17' Processing helix chain 'A' and resid 22 through 30 Processing helix chain 'A' and resid 46 through 61 Processing helix chain 'A' and resid 77 through 83 Processing helix chain 'A' and resid 97 through 106 removed outlier: 3.738A pdb=" N TYR A 104 " --> pdb=" O GLU A 100 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N PHE A 106 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 132 Processing helix chain 'A' and resid 144 through 151 Processing helix chain 'A' and resid 169 through 178 removed outlier: 3.668A pdb=" N ARG A 177 " --> pdb=" O ALA A 173 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N TYR A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 200 Processing helix chain 'A' and resid 205 through 216 removed outlier: 4.557A pdb=" N GLU A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 230 Processing helix chain 'A' and resid 231 through 234 Processing helix chain 'A' and resid 248 through 264 Processing helix chain 'A' and resid 331 through 351 Processing helix chain 'A' and resid 366 through 376 removed outlier: 3.855A pdb=" N VAL A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 463 Processing helix chain 'A' and resid 477 through 482 removed outlier: 4.301A pdb=" N PHE A 482 " --> pdb=" O VAL A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 492 Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.846A pdb=" N TYR A 505 " --> pdb=" O ALA A 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 28 removed outlier: 3.740A pdb=" N THR B 18 " --> pdb=" O ASP B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 39 Processing helix chain 'B' and resid 44 through 56 removed outlier: 4.670A pdb=" N THR B 48 " --> pdb=" O ASP B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 89 Processing helix chain 'B' and resid 109 through 114 removed outlier: 4.111A pdb=" N ARG B 114 " --> pdb=" O ILE B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 138 Processing helix chain 'B' and resid 146 through 159 removed outlier: 3.971A pdb=" N SER B 150 " --> pdb=" O ASP B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 194 Processing helix chain 'B' and resid 199 through 203 Processing helix chain 'B' and resid 219 through 224 Processing helix chain 'B' and resid 227 through 233 removed outlier: 3.945A pdb=" N THR B 232 " --> pdb=" O LYS B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 238 Processing helix chain 'B' and resid 243 through 248 Processing helix chain 'B' and resid 257 through 280 Processing helix chain 'B' and resid 300 through 302 No H-bonds generated for 'chain 'B' and resid 300 through 302' Processing helix chain 'B' and resid 353 through 367 removed outlier: 3.522A pdb=" N GLN B 357 " --> pdb=" O SER B 353 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ASN B 367 " --> pdb=" O LYS B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 384 Processing helix chain 'B' and resid 421 through 436 removed outlier: 4.238A pdb=" N ASP B 432 " --> pdb=" O SER B 428 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ILE B 433 " --> pdb=" O VAL B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 450 removed outlier: 4.056A pdb=" N LEU B 446 " --> pdb=" O ASP B 442 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU B 447 " --> pdb=" O LEU B 443 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 311 through 319 removed outlier: 4.787A pdb=" N CYS A 299 " --> pdb=" O GLY A 315 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N VAL A 317 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ALA A 297 " --> pdb=" O VAL A 317 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N CYS A 279 " --> pdb=" O PHE A 358 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N HIS A 360 " --> pdb=" O CYS A 279 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU A 281 " --> pdb=" O HIS A 360 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N GLY A 385 " --> pdb=" O ASN A 446 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ILE A 412 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N GLU A 3 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LYS B 413 " --> pdb=" O LEU A 4 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N TYR A 6 " --> pdb=" O LYS B 413 " (cutoff:3.500A) removed outlier: 10.487A pdb=" N SER B 415 " --> pdb=" O TYR A 6 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N MET B 414 " --> pdb=" O LYS B 167 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N LYS B 167 " --> pdb=" O MET B 414 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 20 Processing sheet with id=AA3, first strand: chain 'A' and resid 92 through 95 removed outlier: 6.254A pdb=" N GLY A 42 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N ILE A 142 " --> pdb=" O GLY A 42 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL A 44 " --> pdb=" O ILE A 142 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 321 through 322 removed outlier: 3.654A pdb=" N GLU A 327 " --> pdb=" O ASN A 322 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 425 through 426 removed outlier: 3.603A pdb=" N SER A 431 " --> pdb=" O VAL A 426 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 31 through 33 removed outlier: 6.047A pdb=" N ILE B 5 " --> pdb=" O TRP B 33 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LYS B 4 " --> pdb=" O LYS B 59 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N LEU B 61 " --> pdb=" O LYS B 4 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N PHE B 6 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N VAL B 63 " --> pdb=" O PHE B 6 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N SER B 8 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N ILE B 95 " --> pdb=" O CYS B 58 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N PHE B 60 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N LEU B 97 " --> pdb=" O PHE B 60 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE B 62 " --> pdb=" O LEU B 97 " (cutoff:3.500A) removed outlier: 8.648A pdb=" N ILE B 118 " --> pdb=" O ILE B 94 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 283 through 286 removed outlier: 6.706A pdb=" N PHE B 291 " --> pdb=" O ALA B 325 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ALA B 325 " --> pdb=" O PHE B 291 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 283 through 286 removed outlier: 6.706A pdb=" N PHE B 291 " --> pdb=" O ALA B 325 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ALA B 325 " --> pdb=" O PHE B 291 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEU B 402 " --> pdb=" O ILE B 179 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 208 through 210 Processing sheet with id=AB1, first strand: chain 'B' and resid 304 through 305 353 hydrogen bonds defined for protein. 975 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: 1.14 Time building geometry restraints manager: 0.86 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: 2285 1.33 - 1.45: 1241 1.45 - 1.57: 4510 1.57 - 1.69: 0 1.69 - 1.80: 35 Bond restraints: 8071 Sorted by residual: bond pdb=" N TYR B 318 " pdb=" CA TYR B 318 " ideal model delta sigma weight residual 1.455 1.490 -0.035 1.21e-02 6.83e+03 8.40e+00 bond pdb=" CA SER A 175 " pdb=" CB SER A 175 " ideal model delta sigma weight residual 1.528 1.489 0.039 1.37e-02 5.33e+03 8.26e+00 bond pdb=" N LYS B 317 " pdb=" CA LYS B 317 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.15e-02 7.56e+03 8.18e+00 bond pdb=" N GLU A 184 " pdb=" CA GLU A 184 " ideal model delta sigma weight residual 1.457 1.492 -0.036 1.28e-02 6.10e+03 7.79e+00 bond pdb=" N GLU B 13 " pdb=" CA GLU B 13 " ideal model delta sigma weight residual 1.452 1.486 -0.034 1.22e-02 6.72e+03 7.72e+00 ... (remaining 8066 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 10617 1.68 - 3.35: 244 3.35 - 5.03: 32 5.03 - 6.71: 8 6.71 - 8.38: 4 Bond angle restraints: 10905 Sorted by residual: angle pdb=" CA PHE A 183 " pdb=" C PHE A 183 " pdb=" O PHE A 183 " ideal model delta sigma weight residual 122.03 115.16 6.87 1.17e+00 7.31e-01 3.45e+01 angle pdb=" N VAL B 395 " pdb=" CA VAL B 395 " pdb=" C VAL B 395 " ideal model delta sigma weight residual 113.71 108.34 5.37 9.50e-01 1.11e+00 3.20e+01 angle pdb=" C ASP B 191 " pdb=" CA ASP B 191 " pdb=" CB ASP B 191 " ideal model delta sigma weight residual 116.54 110.80 5.74 1.15e+00 7.56e-01 2.49e+01 angle pdb=" C PHE A 183 " pdb=" CA PHE A 183 " pdb=" CB PHE A 183 " ideal model delta sigma weight residual 111.95 104.90 7.05 1.50e+00 4.44e-01 2.21e+01 angle pdb=" N LYS A 174 " pdb=" CA LYS A 174 " pdb=" C LYS A 174 " ideal model delta sigma weight residual 112.38 107.11 5.27 1.22e+00 6.72e-01 1.86e+01 ... (remaining 10900 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 4481 17.56 - 35.13: 313 35.13 - 52.69: 50 52.69 - 70.26: 18 70.26 - 87.82: 6 Dihedral angle restraints: 4868 sinusoidal: 2045 harmonic: 2823 Sorted by residual: dihedral pdb=" CB MET A 406 " pdb=" CG MET A 406 " pdb=" SD MET A 406 " pdb=" CE MET A 406 " ideal model delta sinusoidal sigma weight residual -60.00 -0.13 -59.87 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CB LYS B 196 " pdb=" CG LYS B 196 " pdb=" CD LYS B 196 " pdb=" CE LYS B 196 " ideal model delta sinusoidal sigma weight residual 60.00 119.05 -59.05 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CG ARG A 275 " pdb=" CD ARG A 275 " pdb=" NE ARG A 275 " pdb=" CZ ARG A 275 " ideal model delta sinusoidal sigma weight residual 90.00 131.68 -41.68 2 1.50e+01 4.44e-03 9.43e+00 ... (remaining 4865 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 898 0.048 - 0.096: 194 0.096 - 0.144: 72 0.144 - 0.192: 5 0.192 - 0.240: 2 Chirality restraints: 1171 Sorted by residual: chirality pdb=" CA LEU A 182 " pdb=" N LEU A 182 " pdb=" C LEU A 182 " pdb=" CB LEU A 182 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA GLU A 185 " pdb=" N GLU A 185 " pdb=" C GLU A 185 " pdb=" CB GLU A 185 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA GLU B 13 " pdb=" N GLU B 13 " pdb=" C GLU B 13 " pdb=" CB GLU B 13 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.00e-01 ... (remaining 1168 not shown) Planarity restraints: 1387 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 178 " 0.012 2.00e-02 2.50e+03 2.50e-02 6.26e+00 pdb=" C TYR A 178 " -0.043 2.00e-02 2.50e+03 pdb=" O TYR A 178 " 0.016 2.00e-02 2.50e+03 pdb=" N THR A 179 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 19 " -0.170 9.50e-02 1.11e+02 7.64e-02 3.58e+00 pdb=" NE ARG B 19 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG B 19 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG B 19 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 19 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 177 " 0.148 9.50e-02 1.11e+02 6.64e-02 2.74e+00 pdb=" NE ARG A 177 " -0.008 2.00e-02 2.50e+03 pdb=" CZ ARG A 177 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 177 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG A 177 " 0.006 2.00e-02 2.50e+03 ... (remaining 1384 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 80 2.62 - 3.19: 6447 3.19 - 3.76: 11304 3.76 - 4.33: 16885 4.33 - 4.90: 27845 Nonbonded interactions: 62561 Sorted by model distance: nonbonded pdb=" O TRP A 269 " pdb=" OH TYR A 467 " model vdw 2.047 3.040 nonbonded pdb=" O PHE A 183 " pdb=" CG GLU A 184 " model vdw 2.175 3.440 nonbonded pdb=" O ASN A 34 " pdb=" OH TYR A 261 " model vdw 2.180 3.040 nonbonded pdb=" OD2 ASP A 25 " pdb=" OH TYR B 154 " model vdw 2.239 3.040 nonbonded pdb=" OG1 THR B 66 " pdb=" OD2 ASP B 100 " model vdw 2.261 3.040 ... (remaining 62556 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.660 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: 0.020 Process input model: 8.100 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8071 Z= 0.231 Angle : 0.604 8.382 10905 Z= 0.378 Chirality : 0.047 0.240 1171 Planarity : 0.005 0.076 1387 Dihedral : 12.788 87.820 3042 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.94 % Favored : 96.96 % Rotamer: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.27), residues: 953 helix: 1.39 (0.28), residues: 338 sheet: 0.75 (0.41), residues: 170 loop : -0.42 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 177 TYR 0.023 0.001 TYR B 416 PHE 0.014 0.001 PHE A 425 TRP 0.009 0.001 TRP B 20 HIS 0.005 0.001 HIS B 9 Details of bonding type rmsd covalent geometry : bond 0.00436 ( 8071) covalent geometry : angle 0.60400 (10905) hydrogen bonds : bond 0.17536 ( 347) hydrogen bonds : angle 7.51080 ( 975) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.313 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.0739 time to fit residues: 12.4986 Evaluate side-chains 78 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 49 optimal weight: 0.0270 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.0870 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 overall best weight: 1.8220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 HIS A 374 ASN A 430 GLN ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 GLN B 364 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.101988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.095250 restraints weight = 32833.639| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 4.04 r_work: 0.2776 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8071 Z= 0.128 Angle : 0.500 7.987 10905 Z= 0.267 Chirality : 0.044 0.226 1171 Planarity : 0.004 0.054 1387 Dihedral : 4.038 17.935 1036 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.52 % Favored : 97.38 % Rotamer: Outliers : 1.28 % Allowed : 9.64 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.27), residues: 953 helix: 2.26 (0.28), residues: 331 sheet: 0.90 (0.43), residues: 144 loop : -0.25 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 283 TYR 0.015 0.001 TYR B 330 PHE 0.019 0.001 PHE A 186 TRP 0.035 0.001 TRP B 294 HIS 0.004 0.001 HIS B 320 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 8071) covalent geometry : angle 0.50034 (10905) hydrogen bonds : bond 0.03723 ( 347) hydrogen bonds : angle 5.33316 ( 975) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.299 Fit side-chains REVERT: A 74 MET cc_start: 0.9454 (ppp) cc_final: 0.8673 (ppp) REVERT: A 78 PHE cc_start: 0.8950 (t80) cc_final: 0.8702 (t80) REVERT: A 84 CYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7687 (p) REVERT: A 177 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.8097 (mtt180) REVERT: A 262 TYR cc_start: 0.9216 (t80) cc_final: 0.8992 (t80) REVERT: A 409 ASN cc_start: 0.9292 (m-40) cc_final: 0.9088 (m-40) REVERT: A 435 MET cc_start: 0.9198 (mmm) cc_final: 0.8590 (mmm) outliers start: 11 outliers final: 3 residues processed: 102 average time/residue: 0.0648 time to fit residues: 9.5484 Evaluate side-chains 81 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 177 ARG Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 436 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 13 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 54 optimal weight: 10.0000 chunk 69 optimal weight: 0.1980 chunk 22 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 52 optimal weight: 9.9990 chunk 82 optimal weight: 10.0000 chunk 73 optimal weight: 7.9990 chunk 78 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 overall best weight: 5.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 56 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.094741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.087887 restraints weight = 33016.491| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 3.77 r_work: 0.2706 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 8071 Z= 0.271 Angle : 0.592 9.250 10905 Z= 0.314 Chirality : 0.046 0.220 1171 Planarity : 0.004 0.054 1387 Dihedral : 4.282 20.565 1036 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.62 % Favored : 97.27 % Rotamer: Outliers : 2.09 % Allowed : 9.41 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.27), residues: 953 helix: 2.12 (0.28), residues: 338 sheet: 0.65 (0.43), residues: 138 loop : -0.36 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 177 TYR 0.018 0.002 TYR A 472 PHE 0.020 0.002 PHE A 186 TRP 0.018 0.002 TRP B 294 HIS 0.006 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00627 ( 8071) covalent geometry : angle 0.59228 (10905) hydrogen bonds : bond 0.04214 ( 347) hydrogen bonds : angle 5.38263 ( 975) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 0.339 Fit side-chains REVERT: A 74 MET cc_start: 0.9626 (ppp) cc_final: 0.9190 (ppp) REVERT: A 177 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.8044 (mtt180) REVERT: A 184 GLU cc_start: 0.4363 (OUTLIER) cc_final: 0.2260 (mt-10) REVERT: A 262 TYR cc_start: 0.9445 (t80) cc_final: 0.9149 (t80) REVERT: A 409 ASN cc_start: 0.9462 (m-40) cc_final: 0.9163 (m-40) REVERT: A 451 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7757 (tm-30) outliers start: 18 outliers final: 9 residues processed: 86 average time/residue: 0.0681 time to fit residues: 8.6020 Evaluate side-chains 81 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 177 ARG Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 436 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 73 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 78 optimal weight: 9.9990 chunk 1 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 90 optimal weight: 7.9990 chunk 32 optimal weight: 8.9990 chunk 21 optimal weight: 6.9990 chunk 4 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.094590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.087718 restraints weight = 34159.556| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 3.87 r_work: 0.2708 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 8071 Z= 0.245 Angle : 0.553 8.829 10905 Z= 0.294 Chirality : 0.045 0.300 1171 Planarity : 0.004 0.049 1387 Dihedral : 4.295 20.729 1036 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.36 % Favored : 96.54 % Rotamer: Outliers : 2.21 % Allowed : 10.10 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.27), residues: 953 helix: 2.02 (0.28), residues: 344 sheet: 0.51 (0.43), residues: 138 loop : -0.37 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 177 TYR 0.011 0.002 TYR A 178 PHE 0.021 0.002 PHE A 186 TRP 0.018 0.002 TRP B 294 HIS 0.004 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00564 ( 8071) covalent geometry : angle 0.55277 (10905) hydrogen bonds : bond 0.03931 ( 347) hydrogen bonds : angle 5.28893 ( 975) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 0.353 Fit side-chains REVERT: A 74 MET cc_start: 0.9669 (ppp) cc_final: 0.9251 (ppp) REVERT: A 177 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.7960 (mtt180) REVERT: A 184 GLU cc_start: 0.4222 (OUTLIER) cc_final: 0.2124 (mt-10) REVERT: A 262 TYR cc_start: 0.9482 (t80) cc_final: 0.9191 (t80) REVERT: A 409 ASN cc_start: 0.9520 (m-40) cc_final: 0.9261 (m110) REVERT: A 451 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7848 (tm-30) REVERT: A 472 TYR cc_start: 0.9123 (t80) cc_final: 0.8888 (t80) REVERT: B 294 TRP cc_start: 0.8605 (p-90) cc_final: 0.8015 (p-90) outliers start: 19 outliers final: 11 residues processed: 82 average time/residue: 0.0762 time to fit residues: 9.1464 Evaluate side-chains 82 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 177 ARG Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 436 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 12 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 9 optimal weight: 8.9990 chunk 64 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 86 optimal weight: 9.9990 chunk 82 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.096486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.089561 restraints weight = 32566.516| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 3.80 r_work: 0.2743 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8071 Z= 0.156 Angle : 0.494 8.507 10905 Z= 0.260 Chirality : 0.044 0.220 1171 Planarity : 0.004 0.047 1387 Dihedral : 4.137 21.063 1036 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.04 % Favored : 96.85 % Rotamer: Outliers : 1.63 % Allowed : 10.69 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.27), residues: 953 helix: 2.23 (0.28), residues: 344 sheet: 0.57 (0.41), residues: 147 loop : -0.27 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 177 TYR 0.011 0.001 TYR A 178 PHE 0.018 0.001 PHE A 186 TRP 0.014 0.001 TRP B 294 HIS 0.003 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 8071) covalent geometry : angle 0.49412 (10905) hydrogen bonds : bond 0.03477 ( 347) hydrogen bonds : angle 5.08595 ( 975) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.317 Fit side-chains REVERT: A 74 MET cc_start: 0.9714 (ppp) cc_final: 0.9288 (ppp) REVERT: A 184 GLU cc_start: 0.3899 (OUTLIER) cc_final: 0.1883 (mt-10) REVERT: A 262 TYR cc_start: 0.9457 (t80) cc_final: 0.9145 (t80) REVERT: A 346 TYR cc_start: 0.8928 (t80) cc_final: 0.8674 (t80) REVERT: A 409 ASN cc_start: 0.9537 (m-40) cc_final: 0.9268 (m110) REVERT: A 430 GLN cc_start: 0.9397 (mm-40) cc_final: 0.8768 (mp10) REVERT: A 435 MET cc_start: 0.9203 (mmm) cc_final: 0.8661 (mmm) REVERT: A 451 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7819 (tm-30) REVERT: A 472 TYR cc_start: 0.8996 (t80) cc_final: 0.8756 (t80) REVERT: B 294 TRP cc_start: 0.8675 (p-90) cc_final: 0.8179 (p-90) outliers start: 14 outliers final: 10 residues processed: 80 average time/residue: 0.0786 time to fit residues: 9.2225 Evaluate side-chains 81 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 436 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 19 optimal weight: 6.9990 chunk 78 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 chunk 85 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 1 optimal weight: 8.9990 chunk 76 optimal weight: 7.9990 chunk 80 optimal weight: 5.9990 chunk 7 optimal weight: 0.0970 overall best weight: 4.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.094829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.087913 restraints weight = 33244.286| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 3.80 r_work: 0.2716 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 8071 Z= 0.227 Angle : 0.539 8.165 10905 Z= 0.284 Chirality : 0.044 0.226 1171 Planarity : 0.004 0.048 1387 Dihedral : 4.260 21.486 1036 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.04 % Favored : 96.85 % Rotamer: Outliers : 1.86 % Allowed : 10.45 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.27), residues: 953 helix: 2.11 (0.28), residues: 345 sheet: 0.44 (0.41), residues: 147 loop : -0.33 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 407 TYR 0.013 0.002 TYR A 178 PHE 0.018 0.001 PHE A 425 TRP 0.012 0.001 TRP B 294 HIS 0.004 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00525 ( 8071) covalent geometry : angle 0.53866 (10905) hydrogen bonds : bond 0.03760 ( 347) hydrogen bonds : angle 5.15737 ( 975) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.258 Fit side-chains REVERT: A 74 MET cc_start: 0.9694 (ppp) cc_final: 0.9283 (ppp) REVERT: A 184 GLU cc_start: 0.4020 (OUTLIER) cc_final: 0.2034 (mt-10) REVERT: A 262 TYR cc_start: 0.9509 (t80) cc_final: 0.9184 (t80) REVERT: A 346 TYR cc_start: 0.9008 (t80) cc_final: 0.8733 (t80) REVERT: A 409 ASN cc_start: 0.9540 (m-40) cc_final: 0.9276 (m110) REVERT: A 425 PHE cc_start: 0.7676 (t80) cc_final: 0.7446 (t80) REVERT: A 430 GLN cc_start: 0.9465 (mm-40) cc_final: 0.8630 (mp10) REVERT: A 435 MET cc_start: 0.9195 (mmm) cc_final: 0.8587 (mmm) REVERT: A 451 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.7974 (tm-30) REVERT: A 472 TYR cc_start: 0.9028 (t80) cc_final: 0.8735 (t80) REVERT: B 294 TRP cc_start: 0.8680 (p-90) cc_final: 0.8096 (p-90) outliers start: 16 outliers final: 12 residues processed: 80 average time/residue: 0.0699 time to fit residues: 8.5037 Evaluate side-chains 81 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 436 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 60 optimal weight: 0.7980 chunk 58 optimal weight: 10.0000 chunk 74 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 chunk 16 optimal weight: 0.0570 chunk 45 optimal weight: 1.9990 chunk 28 optimal weight: 8.9990 chunk 72 optimal weight: 0.9990 chunk 85 optimal weight: 9.9990 chunk 23 optimal weight: 0.9990 chunk 50 optimal weight: 9.9990 overall best weight: 0.9704 ------------------------------------------------------------------------------- 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 = 0.2984 r_free = 0.2984 target = 0.099341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.092188 restraints weight = 31232.992| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 3.87 r_work: 0.2799 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8071 Z= 0.093 Angle : 0.469 8.954 10905 Z= 0.243 Chirality : 0.043 0.272 1171 Planarity : 0.004 0.044 1387 Dihedral : 3.991 22.098 1036 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.52 % Favored : 97.38 % Rotamer: Outliers : 1.28 % Allowed : 11.15 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.27), residues: 953 helix: 2.32 (0.28), residues: 351 sheet: 0.53 (0.41), residues: 147 loop : -0.22 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 113 TYR 0.013 0.001 TYR B 293 PHE 0.018 0.001 PHE A 186 TRP 0.013 0.001 TRP A 370 HIS 0.003 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00212 ( 8071) covalent geometry : angle 0.46891 (10905) hydrogen bonds : bond 0.03063 ( 347) hydrogen bonds : angle 4.87336 ( 975) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.325 Fit side-chains REVERT: A 74 MET cc_start: 0.9766 (ppp) cc_final: 0.9348 (ppp) REVERT: A 184 GLU cc_start: 0.3743 (OUTLIER) cc_final: 0.1734 (mt-10) REVERT: A 262 TYR cc_start: 0.9403 (t80) cc_final: 0.9105 (t80) REVERT: A 409 ASN cc_start: 0.9553 (m-40) cc_final: 0.9264 (m110) REVERT: A 435 MET cc_start: 0.9162 (mmm) cc_final: 0.8574 (mmm) REVERT: A 451 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7891 (tm-30) REVERT: A 472 TYR cc_start: 0.8823 (t80) cc_final: 0.8611 (t80) REVERT: B 294 TRP cc_start: 0.8726 (p-90) cc_final: 0.8196 (p-90) outliers start: 11 outliers final: 8 residues processed: 87 average time/residue: 0.0719 time to fit residues: 9.5378 Evaluate side-chains 82 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 436 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 32 optimal weight: 0.9980 chunk 55 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 75 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 74 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 30 optimal weight: 0.4980 chunk 76 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.099466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.092891 restraints weight = 33713.104| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 3.91 r_work: 0.2760 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8071 Z= 0.130 Angle : 0.488 9.722 10905 Z= 0.253 Chirality : 0.043 0.191 1171 Planarity : 0.004 0.046 1387 Dihedral : 3.992 20.769 1036 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.94 % Favored : 96.96 % Rotamer: Outliers : 1.28 % Allowed : 12.08 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.27 (0.27), residues: 953 helix: 2.36 (0.28), residues: 350 sheet: 0.56 (0.41), residues: 148 loop : -0.24 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 407 TYR 0.018 0.001 TYR B 416 PHE 0.033 0.001 PHE A 425 TRP 0.010 0.001 TRP B 294 HIS 0.004 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 8071) covalent geometry : angle 0.48790 (10905) hydrogen bonds : bond 0.03273 ( 347) hydrogen bonds : angle 4.85999 ( 975) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.364 Fit side-chains REVERT: A 9 GLU cc_start: 0.9446 (tp30) cc_final: 0.8677 (tp30) REVERT: A 74 MET cc_start: 0.9749 (ppp) cc_final: 0.9278 (ppp) REVERT: A 184 GLU cc_start: 0.3858 (OUTLIER) cc_final: 0.1849 (mt-10) REVERT: A 262 TYR cc_start: 0.9469 (t80) cc_final: 0.9187 (t80) REVERT: A 346 TYR cc_start: 0.8906 (t80) cc_final: 0.8682 (t80) REVERT: A 407 ARG cc_start: 0.9613 (ttp80) cc_final: 0.9048 (ttp-170) REVERT: A 409 ASN cc_start: 0.9548 (m-40) cc_final: 0.9269 (m110) REVERT: A 413 VAL cc_start: 0.9270 (t) cc_final: 0.9010 (p) REVERT: A 430 GLN cc_start: 0.9470 (mm-40) cc_final: 0.8735 (mp10) REVERT: A 435 MET cc_start: 0.9152 (mmm) cc_final: 0.8536 (mmm) REVERT: A 451 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7943 (tm-30) REVERT: A 464 LYS cc_start: 0.9154 (mmtt) cc_final: 0.8805 (mmtt) REVERT: A 472 TYR cc_start: 0.8846 (t80) cc_final: 0.8500 (t80) REVERT: B 294 TRP cc_start: 0.8678 (p-90) cc_final: 0.8097 (p-90) outliers start: 11 outliers final: 9 residues processed: 82 average time/residue: 0.0669 time to fit residues: 8.4138 Evaluate side-chains 86 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 436 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 93 optimal weight: 10.0000 chunk 62 optimal weight: 8.9990 chunk 83 optimal weight: 0.0570 chunk 36 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 chunk 69 optimal weight: 2.9990 overall best weight: 3.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.097410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.090522 restraints weight = 32605.786| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 3.80 r_work: 0.2762 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8071 Z= 0.166 Angle : 0.511 10.297 10905 Z= 0.264 Chirality : 0.044 0.203 1171 Planarity : 0.004 0.048 1387 Dihedral : 4.067 20.501 1036 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.25 % Favored : 96.64 % Rotamer: Outliers : 1.28 % Allowed : 12.08 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.27), residues: 953 helix: 2.32 (0.28), residues: 345 sheet: 0.57 (0.41), residues: 147 loop : -0.24 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 481 TYR 0.015 0.001 TYR B 416 PHE 0.027 0.001 PHE A 425 TRP 0.010 0.001 TRP B 294 HIS 0.004 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 8071) covalent geometry : angle 0.51076 (10905) hydrogen bonds : bond 0.03454 ( 347) hydrogen bonds : angle 4.93072 ( 975) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.333 Fit side-chains REVERT: A 9 GLU cc_start: 0.9459 (tp30) cc_final: 0.8861 (tp30) REVERT: A 74 MET cc_start: 0.9728 (ppp) cc_final: 0.9276 (ppp) REVERT: A 184 GLU cc_start: 0.3745 (OUTLIER) cc_final: 0.1877 (mt-10) REVERT: A 262 TYR cc_start: 0.9490 (t80) cc_final: 0.9205 (t80) REVERT: A 346 TYR cc_start: 0.8937 (t80) cc_final: 0.8711 (t80) REVERT: A 409 ASN cc_start: 0.9548 (m-40) cc_final: 0.9258 (m110) REVERT: A 430 GLN cc_start: 0.9489 (mm-40) cc_final: 0.8719 (mp10) REVERT: A 435 MET cc_start: 0.9163 (mmm) cc_final: 0.8544 (mmm) REVERT: A 451 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.7998 (tm-30) REVERT: A 472 TYR cc_start: 0.8808 (t80) cc_final: 0.8547 (t80) REVERT: B 294 TRP cc_start: 0.8694 (p-90) cc_final: 0.8118 (p-90) outliers start: 11 outliers final: 7 residues processed: 83 average time/residue: 0.0732 time to fit residues: 9.2184 Evaluate side-chains 83 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 436 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 79 optimal weight: 7.9990 chunk 72 optimal weight: 9.9990 chunk 36 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 chunk 50 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 63 optimal weight: 8.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.097434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.090550 restraints weight = 32860.942| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 3.81 r_work: 0.2764 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8071 Z= 0.166 Angle : 0.514 10.943 10905 Z= 0.265 Chirality : 0.044 0.212 1171 Planarity : 0.004 0.049 1387 Dihedral : 4.103 20.594 1036 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.46 % Favored : 96.43 % Rotamer: Outliers : 1.28 % Allowed : 12.08 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.27), residues: 953 helix: 2.28 (0.28), residues: 345 sheet: 0.57 (0.42), residues: 147 loop : -0.25 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 407 TYR 0.014 0.001 TYR B 293 PHE 0.027 0.001 PHE A 425 TRP 0.015 0.001 TRP B 175 HIS 0.004 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 8071) covalent geometry : angle 0.51405 (10905) hydrogen bonds : bond 0.03447 ( 347) hydrogen bonds : angle 4.94479 ( 975) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1906 Ramachandran restraints generated. 953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.327 Fit side-chains REVERT: A 9 GLU cc_start: 0.9416 (tp30) cc_final: 0.9047 (tp30) REVERT: A 74 MET cc_start: 0.9728 (ppp) cc_final: 0.9283 (ppp) REVERT: A 184 GLU cc_start: 0.3689 (OUTLIER) cc_final: 0.1885 (mt-10) REVERT: A 262 TYR cc_start: 0.9488 (t80) cc_final: 0.9201 (t80) REVERT: A 346 TYR cc_start: 0.8942 (t80) cc_final: 0.8737 (t80) REVERT: A 407 ARG cc_start: 0.9629 (ttp80) cc_final: 0.9423 (ttp80) REVERT: A 409 ASN cc_start: 0.9553 (m-40) cc_final: 0.9259 (m110) REVERT: A 413 VAL cc_start: 0.9252 (t) cc_final: 0.8995 (p) REVERT: A 435 MET cc_start: 0.9164 (mmm) cc_final: 0.8534 (mmm) REVERT: A 451 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8016 (tm-30) REVERT: A 464 LYS cc_start: 0.9160 (mmtt) cc_final: 0.8621 (mmtt) REVERT: A 465 LEU cc_start: 0.9040 (mm) cc_final: 0.8823 (mm) REVERT: A 472 TYR cc_start: 0.8801 (t80) cc_final: 0.7988 (t80) REVERT: B 294 TRP cc_start: 0.8687 (p-90) cc_final: 0.8100 (p-90) outliers start: 11 outliers final: 8 residues processed: 82 average time/residue: 0.0709 time to fit residues: 8.8566 Evaluate side-chains 85 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 436 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 21 optimal weight: 4.9990 chunk 76 optimal weight: 8.9990 chunk 90 optimal weight: 0.9990 chunk 15 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 38 optimal weight: 9.9990 chunk 32 optimal weight: 0.0070 chunk 34 optimal weight: 6.9990 overall best weight: 2.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 9 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.098931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.092037 restraints weight = 32539.863| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 3.83 r_work: 0.2808 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8071 Z= 0.124 Angle : 0.491 11.256 10905 Z= 0.252 Chirality : 0.044 0.226 1171 Planarity : 0.004 0.047 1387 Dihedral : 4.013 21.993 1036 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.15 % Favored : 96.75 % Rotamer: Outliers : 1.05 % Allowed : 12.43 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.27 (0.27), residues: 953 helix: 2.31 (0.28), residues: 351 sheet: 0.64 (0.42), residues: 147 loop : -0.24 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 407 TYR 0.013 0.001 TYR B 293 PHE 0.027 0.001 PHE A 425 TRP 0.013 0.001 TRP B 175 HIS 0.010 0.001 HIS B 9 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 8071) covalent geometry : angle 0.49070 (10905) hydrogen bonds : bond 0.03242 ( 347) hydrogen bonds : angle 4.86091 ( 975) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1606.15 seconds wall clock time: 28 minutes 23.93 seconds (1703.93 seconds total)