Starting phenix.real_space_refine on Wed Mar 12 10:00:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8isy_35700/03_2025/8isy_35700.cif Found real_map, /net/cci-nas-00/data/ceres_data/8isy_35700/03_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_35700/03_2025/8isy_35700.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8isy_35700/03_2025/8isy_35700.map" model { file = "/net/cci-nas-00/data/ceres_data/8isy_35700/03_2025/8isy_35700.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8isy_35700/03_2025/8isy_35700.cif" } resolution = 3.27 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= 0.009 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.13, per 1000 atoms: 0.65 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: 1.91 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.01 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: 3.89 Time building geometry restraints manager: 2.32 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: 3.080 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.560 Find NCS groups from input model: 0.100 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:3.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.790 ------------------------------------------------------------------------------- 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= 0.282 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (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 TRP 0.009 0.001 TRP B 20 HIS 0.005 0.001 HIS B 9 PHE 0.014 0.001 PHE A 425 TYR 0.023 0.001 TYR B 416 ARG 0.003 0.000 ARG A 177 *********************** 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 : 0.900 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.1634 time to fit residues: 27.4915 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 : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 80 optimal weight: 8.9990 chunk 72 optimal weight: 7.9990 chunk 39 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 7.9990 chunk 38 optimal weight: 20.0000 chunk 74 optimal weight: 0.9980 chunk 28 optimal weight: 10.0000 chunk 45 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 86 optimal weight: 7.9990 overall best weight: 3.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 HIS A 430 GLN A 454 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.099325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.092615 restraints weight = 33152.238| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 3.88 r_work: 0.2740 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.1532 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= 0.276 Angle : 0.531 8.021 10905 Z= 0.284 Chirality : 0.045 0.268 1171 Planarity : 0.004 0.057 1387 Dihedral : 4.104 17.555 1036 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.62 % Favored : 97.27 % Rotamer: Outliers : 1.86 % Allowed : 8.94 % Favored : 89.20 % 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: 1.14 (0.27), residues: 953 helix: 2.25 (0.29), residues: 331 sheet: 0.87 (0.43), residues: 144 loop : -0.34 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 294 HIS 0.005 0.001 HIS B 320 PHE 0.020 0.002 PHE A 186 TYR 0.016 0.001 TYR B 330 ARG 0.005 0.001 ARG A 177 *********************** 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 103 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.970 Fit side-chains REVERT: A 74 MET cc_start: 0.9476 (ppp) cc_final: 0.8498 (ppp) REVERT: A 262 TYR cc_start: 0.9266 (t80) cc_final: 0.8933 (t80) REVERT: A 409 ASN cc_start: 0.9323 (m-40) cc_final: 0.9110 (m-40) REVERT: A 435 MET cc_start: 0.9226 (mmm) cc_final: 0.8556 (mmm) REVERT: A 451 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7555 (tm-30) REVERT: B 120 PHE cc_start: 0.9330 (m-80) cc_final: 0.8912 (m-10) REVERT: B 178 ILE cc_start: 0.9370 (mt) cc_final: 0.9168 (mp) REVERT: B 334 VAL cc_start: 0.9686 (OUTLIER) cc_final: 0.9463 (t) REVERT: B 366 LYS cc_start: 0.9035 (ttpt) cc_final: 0.8805 (ttmm) outliers start: 16 outliers final: 6 residues processed: 100 average time/residue: 0.1785 time to fit residues: 25.8192 Evaluate side-chains 84 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 351 ILE 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 47 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 85 optimal weight: 0.4980 chunk 5 optimal weight: 9.9990 chunk 44 optimal weight: 9.9990 chunk 94 optimal weight: 2.9990 chunk 93 optimal weight: 0.0370 chunk 46 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 0.0060 overall best weight: 0.9078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.102775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.095999 restraints weight = 32903.760| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 4.02 r_work: 0.2800 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8071 Z= 0.135 Angle : 0.455 6.558 10905 Z= 0.242 Chirality : 0.043 0.186 1171 Planarity : 0.004 0.053 1387 Dihedral : 3.895 18.682 1036 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.20 % Favored : 97.69 % Rotamer: Outliers : 1.05 % Allowed : 9.52 % Favored : 89.43 % 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: 1.31 (0.27), residues: 953 helix: 2.33 (0.28), residues: 344 sheet: 0.75 (0.41), residues: 156 loop : -0.21 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 294 HIS 0.003 0.001 HIS B 9 PHE 0.016 0.001 PHE A 186 TYR 0.010 0.001 TYR B 330 ARG 0.004 0.000 ARG A 481 *********************** 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 97 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 1.402 Fit side-chains REVERT: A 74 MET cc_start: 0.9615 (ppp) cc_final: 0.8790 (ppp) REVERT: A 262 TYR cc_start: 0.9255 (t80) cc_final: 0.8974 (t80) REVERT: A 409 ASN cc_start: 0.9370 (m-40) cc_final: 0.9084 (m-40) REVERT: A 435 MET cc_start: 0.9144 (mmm) cc_final: 0.8408 (mmm) REVERT: A 464 LYS cc_start: 0.9311 (mmtm) cc_final: 0.9102 (mmtt) REVERT: A 472 TYR cc_start: 0.9061 (t80) cc_final: 0.8523 (t80) REVERT: A 474 ASP cc_start: 0.9354 (OUTLIER) cc_final: 0.9093 (t70) REVERT: B 120 PHE cc_start: 0.9337 (m-80) cc_final: 0.9096 (m-80) REVERT: B 294 TRP cc_start: 0.8564 (p-90) cc_final: 0.7931 (p-90) outliers start: 9 outliers final: 5 residues processed: 93 average time/residue: 0.2045 time to fit residues: 28.0767 Evaluate side-chains 80 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 480 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 24 optimal weight: 5.9990 chunk 70 optimal weight: 10.0000 chunk 87 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 26 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 ASN B 435 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.097840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.091021 restraints weight = 32929.516| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 3.81 r_work: 0.2768 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 8071 Z= 0.292 Angle : 0.511 6.531 10905 Z= 0.271 Chirality : 0.044 0.224 1171 Planarity : 0.004 0.046 1387 Dihedral : 4.016 19.221 1036 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.15 % Favored : 96.75 % Rotamer: Outliers : 1.63 % Allowed : 10.34 % Favored : 88.04 % 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: 1.28 (0.27), residues: 953 helix: 2.33 (0.28), residues: 344 sheet: 0.62 (0.40), residues: 156 loop : -0.20 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 294 HIS 0.004 0.001 HIS A 207 PHE 0.019 0.001 PHE A 186 TYR 0.020 0.001 TYR A 178 ARG 0.003 0.000 ARG A 407 *********************** 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 79 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.924 Fit side-chains REVERT: A 74 MET cc_start: 0.9655 (ppp) cc_final: 0.9149 (ppp) REVERT: A 262 TYR cc_start: 0.9392 (t80) cc_final: 0.9016 (t80) REVERT: A 409 ASN cc_start: 0.9464 (m-40) cc_final: 0.9197 (m110) REVERT: A 472 TYR cc_start: 0.9168 (t80) cc_final: 0.8777 (t80) REVERT: B 294 TRP cc_start: 0.8653 (p-90) cc_final: 0.7959 (p-90) outliers start: 14 outliers final: 8 residues processed: 75 average time/residue: 0.1653 time to fit residues: 19.0538 Evaluate side-chains 71 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 190 LEU 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 479 THR Chi-restraints excluded: chain B residue 287 MET 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 94 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 46 optimal weight: 9.9990 chunk 80 optimal weight: 0.9980 chunk 83 optimal weight: 0.4980 chunk 56 optimal weight: 10.0000 chunk 47 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 64 optimal weight: 0.5980 chunk 29 optimal weight: 9.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- 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 = 0.3005 r_free = 0.3005 target = 0.100385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.093433 restraints weight = 31956.419| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 3.80 r_work: 0.2820 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8071 Z= 0.166 Angle : 0.451 6.203 10905 Z= 0.238 Chirality : 0.043 0.179 1171 Planarity : 0.003 0.043 1387 Dihedral : 3.880 18.820 1036 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.73 % Favored : 97.17 % Rotamer: Outliers : 1.05 % Allowed : 10.92 % Favored : 88.04 % 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: 1.38 (0.28), residues: 953 helix: 2.36 (0.28), residues: 351 sheet: 0.63 (0.41), residues: 151 loop : -0.12 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 370 HIS 0.002 0.001 HIS A 360 PHE 0.017 0.001 PHE A 186 TYR 0.015 0.001 TYR A 178 ARG 0.002 0.000 ARG A 481 *********************** 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 83 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 1.825 Fit side-chains REVERT: A 74 MET cc_start: 0.9705 (ppp) cc_final: 0.8803 (ppp) REVERT: A 262 TYR cc_start: 0.9374 (t80) cc_final: 0.8991 (t80) REVERT: A 409 ASN cc_start: 0.9480 (m-40) cc_final: 0.9187 (m110) REVERT: A 451 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7799 (tm-30) REVERT: A 472 TYR cc_start: 0.9059 (t80) cc_final: 0.8683 (t80) REVERT: B 294 TRP cc_start: 0.8691 (p-90) cc_final: 0.7915 (p-90) outliers start: 9 outliers final: 7 residues processed: 79 average time/residue: 0.2600 time to fit residues: 33.4160 Evaluate side-chains 74 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL 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 479 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 287 MET 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 78 optimal weight: 10.0000 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 79 optimal weight: 9.9990 chunk 56 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 chunk 24 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 = 0.2985 r_free = 0.2985 target = 0.099158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.092244 restraints weight = 32409.832| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 3.76 r_work: 0.2800 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8071 Z= 0.214 Angle : 0.470 7.066 10905 Z= 0.247 Chirality : 0.043 0.170 1171 Planarity : 0.004 0.046 1387 Dihedral : 3.901 18.877 1036 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.94 % Favored : 96.96 % Rotamer: Outliers : 1.39 % Allowed : 11.27 % Favored : 87.34 % 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: 1.35 (0.28), residues: 953 helix: 2.33 (0.28), residues: 351 sheet: 0.62 (0.42), residues: 151 loop : -0.13 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 294 HIS 0.003 0.001 HIS A 207 PHE 0.015 0.001 PHE A 186 TYR 0.016 0.001 TYR A 178 ARG 0.002 0.000 ARG A 481 *********************** 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 79 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.892 Fit side-chains REVERT: A 74 MET cc_start: 0.9705 (ppp) cc_final: 0.9197 (ppp) REVERT: A 262 TYR cc_start: 0.9383 (t80) cc_final: 0.9038 (t80) REVERT: A 409 ASN cc_start: 0.9512 (m-40) cc_final: 0.9222 (m110) REVERT: A 451 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7946 (tm-30) REVERT: A 472 TYR cc_start: 0.8979 (t80) cc_final: 0.8399 (t80) REVERT: B 294 TRP cc_start: 0.8733 (p-90) cc_final: 0.8121 (p-90) outliers start: 12 outliers final: 10 residues processed: 75 average time/residue: 0.1566 time to fit residues: 17.8465 Evaluate side-chains 77 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 237 THR 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 479 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 287 MET 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 7 optimal weight: 0.4980 chunk 47 optimal weight: 0.5980 chunk 88 optimal weight: 8.9990 chunk 69 optimal weight: 0.4980 chunk 41 optimal weight: 7.9990 chunk 23 optimal weight: 8.9990 chunk 20 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 93 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 overall best weight: 2.7184 ------------------------------------------------------------------------------- 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 = 0.2975 r_free = 0.2975 target = 0.098590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.091694 restraints weight = 32429.806| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 3.76 r_work: 0.2794 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8071 Z= 0.233 Angle : 0.475 7.050 10905 Z= 0.250 Chirality : 0.043 0.172 1171 Planarity : 0.004 0.048 1387 Dihedral : 3.947 18.809 1036 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.15 % Favored : 96.75 % 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 (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: 1.30 (0.28), residues: 953 helix: 2.32 (0.28), residues: 351 sheet: 0.66 (0.42), residues: 148 loop : -0.21 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 33 HIS 0.003 0.001 HIS A 207 PHE 0.020 0.001 PHE A 425 TYR 0.020 0.001 TYR A 346 ARG 0.002 0.000 ARG A 481 *********************** 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 83 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 1.173 Fit side-chains REVERT: A 74 MET cc_start: 0.9712 (ppp) cc_final: 0.9229 (ppp) REVERT: A 262 TYR cc_start: 0.9415 (t80) cc_final: 0.9090 (t80) REVERT: A 409 ASN cc_start: 0.9528 (m-40) cc_final: 0.9231 (m110) REVERT: A 451 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7949 (tm-30) REVERT: A 472 TYR cc_start: 0.8999 (t80) cc_final: 0.8509 (t80) REVERT: B 294 TRP cc_start: 0.8739 (p-90) cc_final: 0.8130 (p-90) outliers start: 14 outliers final: 9 residues processed: 78 average time/residue: 0.1545 time to fit residues: 18.4428 Evaluate side-chains 76 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 237 THR 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 479 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 287 MET 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 54 optimal weight: 9.9990 chunk 64 optimal weight: 8.9990 chunk 42 optimal weight: 0.9990 chunk 10 optimal weight: 0.0270 chunk 88 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 81 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 overall best weight: 0.9442 ------------------------------------------------------------------------------- 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 = 0.3035 r_free = 0.3035 target = 0.101854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.094897 restraints weight = 32115.132| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 3.82 r_work: 0.2859 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8071 Z= 0.136 Angle : 0.450 7.195 10905 Z= 0.235 Chirality : 0.043 0.193 1171 Planarity : 0.003 0.043 1387 Dihedral : 3.878 20.969 1036 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.41 % Favored : 97.48 % Rotamer: Outliers : 0.93 % Allowed : 11.50 % 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 (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: 1.39 (0.28), residues: 953 helix: 2.41 (0.28), residues: 352 sheet: 0.82 (0.43), residues: 144 loop : -0.21 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 175 HIS 0.003 0.001 HIS A 207 PHE 0.031 0.001 PHE A 425 TYR 0.015 0.001 TYR B 416 ARG 0.002 0.000 ARG A 481 *********************** 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 84 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.952 Fit side-chains REVERT: A 74 MET cc_start: 0.9739 (ppp) cc_final: 0.9246 (ppp) REVERT: A 262 TYR cc_start: 0.9364 (t80) cc_final: 0.9081 (t80) REVERT: A 409 ASN cc_start: 0.9512 (m-40) cc_final: 0.9200 (m110) REVERT: A 451 GLU cc_start: 0.8217 (tt0) cc_final: 0.7924 (tm-30) REVERT: A 472 TYR cc_start: 0.8891 (t80) cc_final: 0.8272 (t80) REVERT: B 294 TRP cc_start: 0.8765 (p-90) cc_final: 0.8145 (p-90) outliers start: 8 outliers final: 6 residues processed: 82 average time/residue: 0.1757 time to fit residues: 21.0325 Evaluate side-chains 74 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain B residue 43 VAL 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 88 optimal weight: 0.7980 chunk 61 optimal weight: 9.9990 chunk 47 optimal weight: 0.3980 chunk 15 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 79 optimal weight: 7.9990 chunk 92 optimal weight: 9.9990 chunk 68 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.3037 r_free = 0.3037 target = 0.103401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.096759 restraints weight = 32799.377| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 3.97 r_work: 0.2824 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8071 Z= 0.140 Angle : 0.450 8.370 10905 Z= 0.233 Chirality : 0.043 0.216 1171 Planarity : 0.003 0.041 1387 Dihedral : 3.791 20.243 1036 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.83 % Favored : 97.06 % Rotamer: Outliers : 0.81 % Allowed : 11.73 % Favored : 87.46 % 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: 1.43 (0.28), residues: 953 helix: 2.44 (0.28), residues: 352 sheet: 0.80 (0.43), residues: 144 loop : -0.17 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 33 HIS 0.003 0.001 HIS B 320 PHE 0.021 0.001 PHE A 425 TYR 0.017 0.001 TYR B 416 ARG 0.002 0.000 ARG A 481 *********************** 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 84 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.993 Fit side-chains REVERT: A 9 GLU cc_start: 0.9376 (tp30) cc_final: 0.9167 (tp30) REVERT: A 74 MET cc_start: 0.9754 (ppp) cc_final: 0.8848 (ppp) REVERT: A 262 TYR cc_start: 0.9377 (t80) cc_final: 0.9105 (t80) REVERT: A 409 ASN cc_start: 0.9533 (m-40) cc_final: 0.9196 (m110) REVERT: A 435 MET cc_start: 0.9063 (mmm) cc_final: 0.8254 (mmm) REVERT: A 451 GLU cc_start: 0.8239 (tt0) cc_final: 0.7850 (tm-30) REVERT: A 472 TYR cc_start: 0.8922 (t80) cc_final: 0.8406 (t80) REVERT: B 294 TRP cc_start: 0.8723 (p-90) cc_final: 0.8047 (p-90) outliers start: 7 outliers final: 5 residues processed: 83 average time/residue: 0.1624 time to fit residues: 20.3735 Evaluate side-chains 78 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 426 VAL 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 63 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 88 optimal weight: 8.9990 chunk 80 optimal weight: 0.4980 chunk 19 optimal weight: 7.9990 chunk 85 optimal weight: 9.9990 chunk 70 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 chunk 3 optimal weight: 10.0000 chunk 72 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- 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 = 0.3002 r_free = 0.3002 target = 0.099852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.092945 restraints weight = 32545.654| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 3.86 r_work: 0.2819 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8071 Z= 0.216 Angle : 0.477 8.304 10905 Z= 0.248 Chirality : 0.044 0.243 1171 Planarity : 0.003 0.045 1387 Dihedral : 3.884 20.062 1036 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.04 % Favored : 96.85 % Rotamer: Outliers : 0.70 % Allowed : 11.96 % Favored : 87.34 % 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: 1.40 (0.28), residues: 953 helix: 2.43 (0.28), residues: 351 sheet: 0.65 (0.42), residues: 148 loop : -0.15 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 33 HIS 0.003 0.001 HIS A 207 PHE 0.022 0.001 PHE A 186 TYR 0.018 0.001 TYR B 416 ARG 0.002 0.000 ARG A 481 ********************** 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 81 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.893 Fit side-chains REVERT: A 74 MET cc_start: 0.9737 (ppp) cc_final: 0.9232 (ppp) REVERT: A 262 TYR cc_start: 0.9401 (t80) cc_final: 0.9108 (t80) REVERT: A 407 ARG cc_start: 0.9596 (ttp-170) cc_final: 0.9364 (ttp-170) REVERT: A 409 ASN cc_start: 0.9535 (m-40) cc_final: 0.9230 (m110) REVERT: A 451 GLU cc_start: 0.8313 (tt0) cc_final: 0.7992 (tm-30) REVERT: A 472 TYR cc_start: 0.8933 (t80) cc_final: 0.8177 (t80) REVERT: B 294 TRP cc_start: 0.8836 (p-90) cc_final: 0.8078 (p-90) outliers start: 6 outliers final: 6 residues processed: 79 average time/residue: 0.1527 time to fit residues: 18.3829 Evaluate side-chains 77 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 310 LEU 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 57 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 71 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 70 optimal weight: 8.9990 chunk 18 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.3003 r_free = 0.3003 target = 0.101547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.094852 restraints weight = 33231.258| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 4.05 r_work: 0.2794 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 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 : 0.003 0.032 8071 Z= 0.175 Angle : 0.461 7.745 10905 Z= 0.239 Chirality : 0.043 0.225 1171 Planarity : 0.003 0.044 1387 Dihedral : 3.857 20.186 1036 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.73 % Favored : 97.17 % Rotamer: Outliers : 0.70 % Allowed : 11.96 % Favored : 87.34 % 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: 1.40 (0.28), residues: 953 helix: 2.41 (0.28), residues: 353 sheet: 0.66 (0.42), residues: 146 loop : -0.14 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 33 HIS 0.009 0.001 HIS B 320 PHE 0.025 0.001 PHE A 425 TYR 0.012 0.001 TYR B 416 ARG 0.002 0.000 ARG A 481 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3736.56 seconds wall clock time: 67 minutes 31.91 seconds (4051.91 seconds total)