Starting phenix.real_space_refine on Wed Sep 17 03:50:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m2h_63585/09_2025/9m2h_63585.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m2h_63585/09_2025/9m2h_63585.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9m2h_63585/09_2025/9m2h_63585.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m2h_63585/09_2025/9m2h_63585.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9m2h_63585/09_2025/9m2h_63585.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m2h_63585/09_2025/9m2h_63585.map" } resolution = 3.4 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= 0.048 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 20 5.16 5 Cl 1 4.86 5 C 2318 2.51 5 N 545 2.21 5 O 569 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3453 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3441 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 414} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'3C4': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.06, per 1000 atoms: 0.31 Number of scatterers: 3453 At special positions: 0 Unit cell: (77, 59.4, 84.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 20 16.00 O 569 8.00 N 545 7.00 C 2318 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 464 " - pdb=" SG CYS A 467 " distance=2.02 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: 0.46 Conformation dependent library (CDL) restraints added in 155.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 802 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 0 sheets defined 64.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 66 through 75 removed outlier: 3.826A pdb=" N SER A 72 " --> pdb=" O PRO A 68 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLN A 73 " --> pdb=" O TYR A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 106 removed outlier: 3.694A pdb=" N VAL A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU A 82 " --> pdb=" O SER A 78 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLN A 83 " --> pdb=" O GLY A 79 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY A 87 " --> pdb=" O GLN A 83 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N SER A 91 " --> pdb=" O GLY A 87 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ALA A 94 " --> pdb=" O GLY A 90 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL A 102 " --> pdb=" O SER A 98 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR A 104 " --> pdb=" O LEU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 131 removed outlier: 3.971A pdb=" N VAL A 125 " --> pdb=" O GLN A 121 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU A 129 " --> pdb=" O VAL A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 141 removed outlier: 3.702A pdb=" N PHE A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 162 removed outlier: 3.723A pdb=" N PHE A 148 " --> pdb=" O THR A 144 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLN A 153 " --> pdb=" O GLY A 149 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU A 154 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N CYS A 157 " --> pdb=" O GLN A 153 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA A 158 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE A 161 " --> pdb=" O CYS A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 181 removed outlier: 3.809A pdb=" N TYR A 175 " --> pdb=" O ARG A 171 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE A 176 " --> pdb=" O THR A 172 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N CYS A 181 " --> pdb=" O PHE A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 199 removed outlier: 3.554A pdb=" N PHE A 198 " --> pdb=" O ARG A 194 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU A 199 " --> pdb=" O ILE A 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 194 through 199' Processing helix chain 'A' and resid 205 through 217 removed outlier: 3.583A pdb=" N ALA A 212 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 238 removed outlier: 3.705A pdb=" N GLY A 238 " --> pdb=" O LEU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 244 removed outlier: 3.686A pdb=" N LEU A 243 " --> pdb=" O ALA A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 257 removed outlier: 3.605A pdb=" N MET A 256 " --> pdb=" O THR A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 292 removed outlier: 4.606A pdb=" N LEU A 270 " --> pdb=" O LYS A 266 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR A 275 " --> pdb=" O MET A 271 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL A 276 " --> pdb=" O ALA A 272 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N THR A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) Proline residue: A 282 - end of helix removed outlier: 3.529A pdb=" N ALA A 286 " --> pdb=" O PRO A 282 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TRP A 289 " --> pdb=" O ALA A 285 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 295 No H-bonds generated for 'chain 'A' and resid 293 through 295' Processing helix chain 'A' and resid 318 through 341 removed outlier: 3.688A pdb=" N GLN A 322 " --> pdb=" O MET A 318 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE A 324 " --> pdb=" O ILE A 320 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE A 326 " --> pdb=" O GLN A 322 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLY A 327 " --> pdb=" O PHE A 323 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA A 329 " --> pdb=" O THR A 325 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR A 331 " --> pdb=" O GLY A 327 " (cutoff:3.500A) Proline residue: A 332 - end of helix removed outlier: 3.909A pdb=" N GLU A 338 " --> pdb=" O TYR A 334 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL A 340 " --> pdb=" O VAL A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 353 removed outlier: 3.986A pdb=" N ARG A 352 " --> pdb=" O SER A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 370 Proline residue: A 362 - end of helix removed outlier: 3.854A pdb=" N ALA A 367 " --> pdb=" O ILE A 363 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ILE A 368 " --> pdb=" O TRP A 364 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE A 369 " --> pdb=" O PHE A 365 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N PHE A 370 " --> pdb=" O LEU A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 384 removed outlier: 3.601A pdb=" N ALA A 379 " --> pdb=" O PRO A 375 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU A 383 " --> pdb=" O ALA A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 390 Processing helix chain 'A' and resid 391 through 401 removed outlier: 4.440A pdb=" N HIS A 397 " --> pdb=" O PRO A 393 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N MET A 398 " --> pdb=" O SER A 394 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR A 400 " --> pdb=" O ALA A 396 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TYR A 401 " --> pdb=" O HIS A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 409 removed outlier: 3.938A pdb=" N ASN A 409 " --> pdb=" O SER A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 439 removed outlier: 3.763A pdb=" N TYR A 425 " --> pdb=" O TRP A 421 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU A 427 " --> pdb=" O ALA A 423 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N VAL A 431 " --> pdb=" O LEU A 427 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE A 437 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 459 removed outlier: 3.619A pdb=" N VAL A 448 " --> pdb=" O GLY A 444 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL A 455 " --> pdb=" O PHE A 451 " (cutoff:3.500A) 116 hydrogen bonds defined for protein. 348 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.52 Time building geometry restraints manager: 0.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 499 1.31 - 1.43: 1154 1.43 - 1.56: 1887 1.56 - 1.69: 0 1.69 - 1.81: 32 Bond restraints: 3572 Sorted by residual: bond pdb=" CA GLN A 62 " pdb=" C GLN A 62 " ideal model delta sigma weight residual 1.520 1.440 0.080 1.39e-02 5.18e+03 3.30e+01 bond pdb=" CA VAL A 125 " pdb=" C VAL A 125 " ideal model delta sigma weight residual 1.524 1.449 0.074 1.30e-02 5.92e+03 3.28e+01 bond pdb=" C GLN A 62 " pdb=" O GLN A 62 " ideal model delta sigma weight residual 1.236 1.181 0.054 1.31e-02 5.83e+03 1.72e+01 bond pdb=" CA ASP A 345 " pdb=" C ASP A 345 " ideal model delta sigma weight residual 1.522 1.472 0.050 1.20e-02 6.94e+03 1.71e+01 bond pdb=" CA VAL A 125 " pdb=" CB VAL A 125 " ideal model delta sigma weight residual 1.540 1.490 0.050 1.29e-02 6.01e+03 1.48e+01 ... (remaining 3567 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 4694 2.74 - 5.48: 153 5.48 - 8.21: 21 8.21 - 10.95: 5 10.95 - 13.69: 2 Bond angle restraints: 4875 Sorted by residual: angle pdb=" N TRP A 122 " pdb=" CA TRP A 122 " pdb=" C TRP A 122 " ideal model delta sigma weight residual 112.38 122.22 -9.84 1.22e+00 6.72e-01 6.50e+01 angle pdb=" C SER A 348 " pdb=" CA SER A 348 " pdb=" CB SER A 348 " ideal model delta sigma weight residual 112.43 98.74 13.69 1.91e+00 2.74e-01 5.14e+01 angle pdb=" N GLY A 75 " pdb=" CA GLY A 75 " pdb=" C GLY A 75 " ideal model delta sigma weight residual 112.08 105.17 6.91 1.01e+00 9.80e-01 4.69e+01 angle pdb=" CA TRP A 122 " pdb=" CB TRP A 122 " pdb=" CG TRP A 122 " ideal model delta sigma weight residual 113.60 126.47 -12.87 1.90e+00 2.77e-01 4.58e+01 angle pdb=" N VAL A 315 " pdb=" CA VAL A 315 " pdb=" C VAL A 315 " ideal model delta sigma weight residual 113.43 107.25 6.18 1.09e+00 8.42e-01 3.22e+01 ... (remaining 4870 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.60: 1691 10.60 - 21.20: 240 21.20 - 31.80: 36 31.80 - 42.40: 16 42.40 - 53.00: 5 Dihedral angle restraints: 1988 sinusoidal: 734 harmonic: 1254 Sorted by residual: dihedral pdb=" C SER A 348 " pdb=" N SER A 348 " pdb=" CA SER A 348 " pdb=" CB SER A 348 " ideal model delta harmonic sigma weight residual -122.60 -105.25 -17.35 0 2.50e+00 1.60e-01 4.82e+01 dihedral pdb=" CA LEU A 130 " pdb=" C LEU A 130 " pdb=" N GLY A 131 " pdb=" CA GLY A 131 " ideal model delta harmonic sigma weight residual 180.00 152.83 27.17 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA PRO A 414 " pdb=" C PRO A 414 " pdb=" N PRO A 415 " pdb=" CA PRO A 415 " ideal model delta harmonic sigma weight residual -180.00 -158.40 -21.60 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 1985 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 423 0.074 - 0.148: 96 0.148 - 0.222: 15 0.222 - 0.296: 2 0.296 - 0.370: 1 Chirality restraints: 537 Sorted by residual: chirality pdb=" CA SER A 348 " pdb=" N SER A 348 " pdb=" C SER A 348 " pdb=" CB SER A 348 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.43e+00 chirality pdb=" CB VAL A 359 " pdb=" CA VAL A 359 " pdb=" CG1 VAL A 359 " pdb=" CG2 VAL A 359 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CB VAL A 63 " pdb=" CA VAL A 63 " pdb=" CG1 VAL A 63 " pdb=" CG2 VAL A 63 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 534 not shown) Planarity restraints: 588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 187 " -0.045 5.00e-02 4.00e+02 6.76e-02 7.32e+00 pdb=" N PRO A 188 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 188 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 188 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 374 " 0.044 5.00e-02 4.00e+02 6.66e-02 7.09e+00 pdb=" N PRO A 375 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 375 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 375 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 392 " -0.038 5.00e-02 4.00e+02 5.63e-02 5.07e+00 pdb=" N PRO A 393 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 393 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 393 " -0.032 5.00e-02 4.00e+02 ... (remaining 585 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 1046 2.81 - 3.33: 2880 3.33 - 3.85: 5265 3.85 - 4.38: 6402 4.38 - 4.90: 10876 Nonbonded interactions: 26469 Sorted by model distance: nonbonded pdb=" O PHE A 246 " pdb=" OH TYR A 390 " model vdw 2.284 3.040 nonbonded pdb=" OG SER A 227 " pdb=" OD2 ASP A 293 " model vdw 2.310 3.040 nonbonded pdb=" O TYR A 95 " pdb=" OG SER A 98 " model vdw 2.343 3.040 nonbonded pdb=" O THR A 237 " pdb=" OG SER A 378 " model vdw 2.358 3.040 nonbonded pdb=" OG SER A 78 " pdb=" OH TYR A 235 " model vdw 2.359 3.040 ... (remaining 26464 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.190 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.830 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 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 : 0.011 0.080 3573 Z= 0.519 Angle : 1.215 13.691 4877 Z= 0.702 Chirality : 0.066 0.370 537 Planarity : 0.009 0.068 588 Dihedral : 10.754 52.999 1183 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.03 % Favored : 92.74 % Rotamer: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Cbeta Deviations : 0.25 % 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: -6.52 (0.24), residues: 427 helix: -4.61 (0.14), residues: 277 sheet: None (None), residues: 0 loop : -3.30 (0.40), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 356 TYR 0.027 0.004 TYR A 163 PHE 0.029 0.004 PHE A 123 TRP 0.036 0.004 TRP A 122 HIS 0.005 0.002 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.01059 ( 3572) covalent geometry : angle 1.21424 ( 4875) SS BOND : bond 0.00686 ( 1) SS BOND : angle 2.08032 ( 2) hydrogen bonds : bond 0.35162 ( 116) hydrogen bonds : angle 12.37714 ( 348) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.161 Fit side-chains revert: symmetry clash REVERT: A 323 PHE cc_start: 0.7272 (t80) cc_final: 0.6869 (t80) REVERT: A 364 TRP cc_start: 0.7663 (t60) cc_final: 0.7377 (t60) REVERT: A 426 VAL cc_start: 0.8849 (t) cc_final: 0.8590 (m) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0686 time to fit residues: 7.0340 Evaluate side-chains 63 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 0.0670 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.4980 chunk 30 optimal weight: 0.0970 chunk 22 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 HIS A 59 GLN ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 HIS A 344 HIS A 428 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.148901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.128596 restraints weight = 4485.436| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.06 r_work: 0.3317 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3573 Z= 0.137 Angle : 0.613 6.856 4877 Z= 0.332 Chirality : 0.041 0.130 537 Planarity : 0.006 0.058 588 Dihedral : 6.654 50.074 464 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.81 % Allowed : 10.96 % Favored : 86.24 % 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: -5.40 (0.29), residues: 427 helix: -3.47 (0.21), residues: 294 sheet: None (None), residues: 0 loop : -3.35 (0.43), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 311 TYR 0.015 0.001 TYR A 267 PHE 0.012 0.002 PHE A 370 TRP 0.010 0.001 TRP A 289 HIS 0.002 0.000 HIS A 321 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 3572) covalent geometry : angle 0.61283 ( 4875) SS BOND : bond 0.00097 ( 1) SS BOND : angle 0.33091 ( 2) hydrogen bonds : bond 0.06596 ( 116) hydrogen bonds : angle 6.67392 ( 348) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.123 Fit side-chains revert: symmetry clash REVERT: A 76 MET cc_start: 0.7823 (tpp) cc_final: 0.7553 (tpp) REVERT: A 364 TRP cc_start: 0.8102 (t60) cc_final: 0.7702 (t60) outliers start: 10 outliers final: 7 residues processed: 66 average time/residue: 0.0617 time to fit residues: 5.0902 Evaluate side-chains 61 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 191 HIS Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 339 LYS Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 436 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 20 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 42 optimal weight: 0.0370 chunk 11 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 40 optimal weight: 0.3980 chunk 17 optimal weight: 0.4980 chunk 12 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.152552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.132158 restraints weight = 4433.118| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.02 r_work: 0.3283 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3573 Z= 0.129 Angle : 0.546 6.023 4877 Z= 0.296 Chirality : 0.040 0.122 537 Planarity : 0.005 0.048 588 Dihedral : 5.999 49.461 464 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.25 % Allowed : 14.04 % Favored : 83.71 % 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: -4.54 (0.33), residues: 427 helix: -2.74 (0.24), residues: 295 sheet: None (None), residues: 0 loop : -3.20 (0.44), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 356 TYR 0.015 0.001 TYR A 267 PHE 0.012 0.001 PHE A 370 TRP 0.011 0.001 TRP A 122 HIS 0.006 0.001 HIS A 191 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 3572) covalent geometry : angle 0.54634 ( 4875) SS BOND : bond 0.00082 ( 1) SS BOND : angle 0.17340 ( 2) hydrogen bonds : bond 0.05524 ( 116) hydrogen bonds : angle 5.96900 ( 348) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.127 Fit side-chains REVERT: A 76 MET cc_start: 0.7594 (tpp) cc_final: 0.7355 (tpp) REVERT: A 105 ARG cc_start: 0.8109 (mmm-85) cc_final: 0.7813 (mmm-85) REVERT: A 364 TRP cc_start: 0.8213 (t60) cc_final: 0.7864 (t60) outliers start: 8 outliers final: 8 residues processed: 69 average time/residue: 0.0614 time to fit residues: 5.4421 Evaluate side-chains 62 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 191 HIS Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 339 LYS Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 436 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 39 optimal weight: 0.3980 chunk 13 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 19 optimal weight: 0.0030 chunk 33 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 22 optimal weight: 0.0870 chunk 4 optimal weight: 0.6980 overall best weight: 0.3768 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.152114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.131920 restraints weight = 4326.003| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.01 r_work: 0.3338 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3573 Z= 0.113 Angle : 0.518 5.514 4877 Z= 0.279 Chirality : 0.039 0.116 537 Planarity : 0.004 0.046 588 Dihedral : 5.549 45.622 464 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.65 % Allowed : 15.17 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.91 (0.36), residues: 427 helix: -2.26 (0.27), residues: 294 sheet: None (None), residues: 0 loop : -3.01 (0.47), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 311 TYR 0.016 0.001 TYR A 267 PHE 0.010 0.001 PHE A 370 TRP 0.010 0.001 TRP A 122 HIS 0.006 0.001 HIS A 191 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 3572) covalent geometry : angle 0.51780 ( 4875) SS BOND : bond 0.00086 ( 1) SS BOND : angle 0.05460 ( 2) hydrogen bonds : bond 0.04724 ( 116) hydrogen bonds : angle 5.60616 ( 348) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.135 Fit side-chains REVERT: A 62 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.8191 (pt0) REVERT: A 105 ARG cc_start: 0.8075 (mmm-85) cc_final: 0.7534 (mmt90) REVERT: A 261 LYS cc_start: 0.7045 (ttpt) cc_final: 0.6695 (tttp) REVERT: A 364 TRP cc_start: 0.8236 (t60) cc_final: 0.7897 (t60) outliers start: 13 outliers final: 9 residues processed: 70 average time/residue: 0.0744 time to fit residues: 6.4183 Evaluate side-chains 66 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 339 LYS Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 436 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 20 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 31 optimal weight: 0.0970 chunk 24 optimal weight: 0.6980 chunk 40 optimal weight: 0.4980 chunk 25 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 2 optimal weight: 0.0970 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.155716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.135185 restraints weight = 4431.215| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.05 r_work: 0.3318 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3573 Z= 0.112 Angle : 0.501 5.207 4877 Z= 0.269 Chirality : 0.039 0.113 537 Planarity : 0.004 0.044 588 Dihedral : 5.205 44.458 464 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 4.49 % Allowed : 14.33 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.41 (0.37), residues: 427 helix: -1.87 (0.28), residues: 294 sheet: None (None), residues: 0 loop : -2.82 (0.48), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 453 TYR 0.018 0.001 TYR A 267 PHE 0.009 0.001 PHE A 417 TRP 0.009 0.001 TRP A 122 HIS 0.003 0.001 HIS A 191 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 3572) covalent geometry : angle 0.50121 ( 4875) SS BOND : bond 0.00088 ( 1) SS BOND : angle 0.09065 ( 2) hydrogen bonds : bond 0.04484 ( 116) hydrogen bonds : angle 5.37148 ( 348) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.076 Fit side-chains REVERT: A 62 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.8202 (pt0) REVERT: A 105 ARG cc_start: 0.8009 (mmm-85) cc_final: 0.7482 (mmt90) REVERT: A 134 TRP cc_start: 0.8539 (m100) cc_final: 0.7977 (m100) REVERT: A 195 ILE cc_start: 0.8905 (tp) cc_final: 0.8597 (tp) REVERT: A 364 TRP cc_start: 0.8235 (t60) cc_final: 0.7917 (t60) REVERT: A 418 MET cc_start: 0.7022 (mtp) cc_final: 0.6635 (mtp) outliers start: 16 outliers final: 13 residues processed: 75 average time/residue: 0.0634 time to fit residues: 5.9819 Evaluate side-chains 70 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 133 TYR Chi-restraints excluded: chain A residue 191 HIS Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 339 LYS Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 436 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 22 optimal weight: 0.0070 chunk 39 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 36 optimal weight: 0.3980 chunk 33 optimal weight: 0.3980 chunk 27 optimal weight: 0.0000 chunk 40 optimal weight: 0.2980 chunk 23 optimal weight: 0.5980 overall best weight: 0.2202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.158893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.138264 restraints weight = 4327.724| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.04 r_work: 0.3321 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3573 Z= 0.095 Angle : 0.501 6.241 4877 Z= 0.265 Chirality : 0.040 0.125 537 Planarity : 0.004 0.045 588 Dihedral : 4.977 42.829 464 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.37 % Allowed : 16.57 % Favored : 80.06 % 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: -3.05 (0.38), residues: 427 helix: -1.57 (0.29), residues: 292 sheet: None (None), residues: 0 loop : -2.74 (0.48), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 453 TYR 0.019 0.001 TYR A 267 PHE 0.008 0.001 PHE A 417 TRP 0.009 0.001 TRP A 122 HIS 0.006 0.001 HIS A 191 Details of bonding type rmsd covalent geometry : bond 0.00203 ( 3572) covalent geometry : angle 0.50075 ( 4875) SS BOND : bond 0.00095 ( 1) SS BOND : angle 0.20763 ( 2) hydrogen bonds : bond 0.04123 ( 116) hydrogen bonds : angle 5.18989 ( 348) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.136 Fit side-chains REVERT: A 62 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.8182 (pt0) REVERT: A 134 TRP cc_start: 0.8466 (m100) cc_final: 0.7891 (m100) REVERT: A 195 ILE cc_start: 0.8854 (tp) cc_final: 0.8535 (tp) REVERT: A 225 LYS cc_start: 0.6761 (mtmp) cc_final: 0.6535 (mttm) REVERT: A 364 TRP cc_start: 0.8193 (t60) cc_final: 0.7887 (t60) REVERT: A 418 MET cc_start: 0.6989 (mtp) cc_final: 0.6586 (mtp) outliers start: 12 outliers final: 11 residues processed: 70 average time/residue: 0.0711 time to fit residues: 6.2214 Evaluate side-chains 70 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 133 TYR Chi-restraints excluded: chain A residue 191 HIS Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 339 LYS Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 436 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 22 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.154949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.134378 restraints weight = 4470.263| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.05 r_work: 0.3276 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3573 Z= 0.133 Angle : 0.521 5.046 4877 Z= 0.276 Chirality : 0.041 0.115 537 Planarity : 0.004 0.044 588 Dihedral : 5.075 43.262 464 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.65 % Allowed : 16.29 % Favored : 80.06 % 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: -2.99 (0.38), residues: 427 helix: -1.53 (0.29), residues: 293 sheet: None (None), residues: 0 loop : -2.74 (0.48), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 453 TYR 0.016 0.001 TYR A 267 PHE 0.009 0.001 PHE A 328 TRP 0.008 0.001 TRP A 122 HIS 0.006 0.001 HIS A 191 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 3572) covalent geometry : angle 0.52091 ( 4875) SS BOND : bond 0.00072 ( 1) SS BOND : angle 0.03382 ( 2) hydrogen bonds : bond 0.04413 ( 116) hydrogen bonds : angle 5.32665 ( 348) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.134 Fit side-chains REVERT: A 62 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.8209 (pt0) REVERT: A 134 TRP cc_start: 0.8549 (m100) cc_final: 0.7956 (m100) REVERT: A 195 ILE cc_start: 0.8826 (tp) cc_final: 0.8382 (tp) REVERT: A 225 LYS cc_start: 0.6848 (mtmp) cc_final: 0.6546 (mttm) REVERT: A 364 TRP cc_start: 0.8231 (t60) cc_final: 0.7928 (t60) REVERT: A 418 MET cc_start: 0.7068 (mtp) cc_final: 0.6669 (mtp) outliers start: 13 outliers final: 12 residues processed: 69 average time/residue: 0.0714 time to fit residues: 6.0853 Evaluate side-chains 69 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 133 TYR Chi-restraints excluded: chain A residue 191 HIS Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 339 LYS Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 436 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 0 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3672 r_free = 0.3672 target = 0.151255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.130523 restraints weight = 4528.972| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.07 r_work: 0.3264 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3573 Z= 0.168 Angle : 0.552 5.407 4877 Z= 0.293 Chirality : 0.043 0.122 537 Planarity : 0.004 0.043 588 Dihedral : 5.294 44.793 464 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.37 % Allowed : 17.13 % Favored : 79.49 % 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: -2.99 (0.38), residues: 427 helix: -1.53 (0.29), residues: 293 sheet: None (None), residues: 0 loop : -2.75 (0.48), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 356 TYR 0.015 0.001 TYR A 267 PHE 0.012 0.002 PHE A 328 TRP 0.007 0.001 TRP A 122 HIS 0.003 0.001 HIS A 191 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 3572) covalent geometry : angle 0.55206 ( 4875) SS BOND : bond 0.00076 ( 1) SS BOND : angle 0.05283 ( 2) hydrogen bonds : bond 0.04777 ( 116) hydrogen bonds : angle 5.45682 ( 348) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.133 Fit side-chains REVERT: A 62 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.8199 (pt0) REVERT: A 134 TRP cc_start: 0.8609 (m100) cc_final: 0.8138 (m100) REVERT: A 195 ILE cc_start: 0.8900 (tp) cc_final: 0.8487 (tp) REVERT: A 225 LYS cc_start: 0.6975 (mtmp) cc_final: 0.6711 (mttm) REVERT: A 364 TRP cc_start: 0.8265 (t60) cc_final: 0.7964 (t60) REVERT: A 418 MET cc_start: 0.7131 (mtp) cc_final: 0.6735 (mtp) outliers start: 12 outliers final: 11 residues processed: 67 average time/residue: 0.0646 time to fit residues: 5.4385 Evaluate side-chains 68 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 133 TYR Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 339 LYS Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 436 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 39 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 3 optimal weight: 0.1980 chunk 14 optimal weight: 0.0170 chunk 36 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 33 optimal weight: 0.4980 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.156516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.136140 restraints weight = 4346.095| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.00 r_work: 0.3312 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3573 Z= 0.104 Angle : 0.500 4.930 4877 Z= 0.265 Chirality : 0.040 0.112 537 Planarity : 0.004 0.044 588 Dihedral : 4.915 43.095 464 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.65 % Allowed : 16.85 % Favored : 79.49 % 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: -2.68 (0.39), residues: 427 helix: -1.27 (0.30), residues: 293 sheet: None (None), residues: 0 loop : -2.67 (0.49), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 453 TYR 0.016 0.001 TYR A 267 PHE 0.008 0.001 PHE A 417 TRP 0.010 0.001 TRP A 122 HIS 0.003 0.000 HIS A 191 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 3572) covalent geometry : angle 0.49976 ( 4875) SS BOND : bond 0.00104 ( 1) SS BOND : angle 0.16376 ( 2) hydrogen bonds : bond 0.04107 ( 116) hydrogen bonds : angle 5.21208 ( 348) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.136 Fit side-chains REVERT: A 62 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.8189 (pt0) REVERT: A 134 TRP cc_start: 0.8505 (m100) cc_final: 0.7965 (m100) REVERT: A 225 LYS cc_start: 0.6908 (mtmp) cc_final: 0.6684 (mttm) REVERT: A 364 TRP cc_start: 0.8190 (t60) cc_final: 0.7898 (t60) REVERT: A 418 MET cc_start: 0.7155 (mtp) cc_final: 0.6793 (mtp) outliers start: 13 outliers final: 11 residues processed: 72 average time/residue: 0.0660 time to fit residues: 5.9939 Evaluate side-chains 71 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 133 TYR Chi-restraints excluded: chain A residue 191 HIS Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 339 LYS Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 436 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 9 optimal weight: 0.4980 chunk 12 optimal weight: 0.0270 chunk 15 optimal weight: 0.1980 chunk 11 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 30 optimal weight: 0.0670 chunk 22 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 overall best weight: 0.2776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 62 GLN ** 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 = 0.3780 r_free = 0.3780 target = 0.159725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.139156 restraints weight = 4374.051| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.02 r_work: 0.3356 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3573 Z= 0.097 Angle : 0.491 5.036 4877 Z= 0.261 Chirality : 0.040 0.112 537 Planarity : 0.004 0.044 588 Dihedral : 4.801 41.995 464 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.53 % Allowed : 18.54 % Favored : 78.93 % 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: -2.36 (0.39), residues: 427 helix: -1.05 (0.30), residues: 296 sheet: None (None), residues: 0 loop : -2.51 (0.50), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 194 TYR 0.016 0.001 TYR A 267 PHE 0.016 0.001 PHE A 440 TRP 0.010 0.001 TRP A 122 HIS 0.002 0.000 HIS A 191 Details of bonding type rmsd covalent geometry : bond 0.00213 ( 3572) covalent geometry : angle 0.49130 ( 4875) SS BOND : bond 0.00090 ( 1) SS BOND : angle 0.18816 ( 2) hydrogen bonds : bond 0.03900 ( 116) hydrogen bonds : angle 5.14953 ( 348) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 854 Ramachandran restraints generated. 427 Oldfield, 0 Emsley, 427 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.123 Fit side-chains REVERT: A 62 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.8139 (pt0) REVERT: A 134 TRP cc_start: 0.8480 (m100) cc_final: 0.7933 (m100) REVERT: A 225 LYS cc_start: 0.6955 (mtmp) cc_final: 0.6705 (mttm) REVERT: A 338 GLU cc_start: 0.7382 (mt-10) cc_final: 0.7175 (mm-30) REVERT: A 364 TRP cc_start: 0.8185 (t60) cc_final: 0.7906 (t60) REVERT: A 418 MET cc_start: 0.7139 (mtp) cc_final: 0.6877 (mtp) outliers start: 9 outliers final: 7 residues processed: 64 average time/residue: 0.0734 time to fit residues: 5.8584 Evaluate side-chains 64 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 133 TYR Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 339 LYS Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 436 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 24 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 9 optimal weight: 0.4980 chunk 3 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.154774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.134216 restraints weight = 4404.755| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.02 r_work: 0.3286 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3573 Z= 0.139 Angle : 0.528 5.391 4877 Z= 0.279 Chirality : 0.042 0.119 537 Planarity : 0.004 0.041 588 Dihedral : 4.981 43.182 464 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.53 % Allowed : 18.82 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.37 (0.39), residues: 427 helix: -1.06 (0.30), residues: 296 sheet: None (None), residues: 0 loop : -2.51 (0.51), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 356 TYR 0.014 0.001 TYR A 267 PHE 0.015 0.001 PHE A 440 TRP 0.007 0.001 TRP A 209 HIS 0.002 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 3572) covalent geometry : angle 0.52818 ( 4875) SS BOND : bond 0.00070 ( 1) SS BOND : angle 0.04193 ( 2) hydrogen bonds : bond 0.04387 ( 116) hydrogen bonds : angle 5.24558 ( 348) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1139.97 seconds wall clock time: 20 minutes 15.65 seconds (1215.65 seconds total)