Starting phenix.real_space_refine on Wed Jun 4 16:22:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m2h_63585/06_2025/9m2h_63585.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m2h_63585/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9m2h_63585/06_2025/9m2h_63585.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m2h_63585/06_2025/9m2h_63585.map" model { file = "/net/cci-nas-00/data/ceres_data/9m2h_63585/06_2025/9m2h_63585.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m2h_63585/06_2025/9m2h_63585.cif" } resolution = 3.4 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= 0.048 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 2.85, per 1000 atoms: 0.83 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: 0.80 Conformation dependent library (CDL) restraints added in 373.1 milliseconds 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: 0.33 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: 0.86 Time building geometry restraints manager: 0.90 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: 2.170 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: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.140 Find NCS groups from input model: 0.040 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.510 ------------------------------------------------------------------------------- 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 (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: -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 TRP 0.036 0.004 TRP A 122 HIS 0.005 0.002 HIS A 249 PHE 0.029 0.004 PHE A 123 TYR 0.027 0.004 TYR A 163 ARG 0.017 0.001 ARG A 356 Details of bonding type rmsd hydrogen bonds : bond 0.35162 ( 116) hydrogen bonds : angle 12.37714 ( 348) SS BOND : bond 0.00686 ( 1) SS BOND : angle 2.08032 ( 2) covalent geometry : bond 0.01059 ( 3572) covalent geometry : angle 1.21424 ( 4875) *********************** 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 : 0.391 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: 0.1578 time to fit residues: 16.1108 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 : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 36 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 25 optimal weight: 0.0980 chunk 39 optimal weight: 0.9980 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 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 = 0.3659 r_free = 0.3659 target = 0.149746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.130141 restraints weight = 4402.536| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.96 r_work: 0.3296 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.2022 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= 0.161 Angle : 0.635 6.957 4877 Z= 0.344 Chirality : 0.042 0.133 537 Planarity : 0.006 0.057 588 Dihedral : 6.755 51.229 464 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.81 % Allowed : 11.24 % Favored : 85.96 % 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: -5.43 (0.29), residues: 427 helix: -3.48 (0.21), residues: 295 sheet: None (None), residues: 0 loop : -3.38 (0.43), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 122 HIS 0.002 0.001 HIS A 249 PHE 0.012 0.002 PHE A 370 TYR 0.015 0.001 TYR A 267 ARG 0.003 0.001 ARG A 356 Details of bonding type rmsd hydrogen bonds : bond 0.06698 ( 116) hydrogen bonds : angle 6.70899 ( 348) SS BOND : bond 0.00056 ( 1) SS BOND : angle 0.52565 ( 2) covalent geometry : bond 0.00361 ( 3572) covalent geometry : angle 0.63511 ( 4875) *********************** 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 68 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.324 Fit side-chains REVERT: A 76 MET cc_start: 0.7838 (tpp) cc_final: 0.7569 (tpp) REVERT: A 323 PHE cc_start: 0.7824 (t80) cc_final: 0.7532 (t80) REVERT: A 364 TRP cc_start: 0.8130 (t60) cc_final: 0.7796 (t60) outliers start: 10 outliers final: 7 residues processed: 64 average time/residue: 0.1404 time to fit residues: 11.3864 Evaluate side-chains 59 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.325 ------------------------------------------------------------------------------- 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 1 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 25 optimal weight: 0.2980 chunk 31 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 overall best weight: 0.6182 ------------------------------------------------------------------------------- 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 = 0.3700 r_free = 0.3700 target = 0.152743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.132310 restraints weight = 4398.876| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.05 r_work: 0.3273 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3573 Z= 0.142 Angle : 0.567 6.239 4877 Z= 0.307 Chirality : 0.041 0.126 537 Planarity : 0.005 0.048 588 Dihedral : 6.141 50.899 464 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.81 % Allowed : 13.20 % Favored : 83.99 % 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: -4.53 (0.33), residues: 427 helix: -2.74 (0.25), residues: 296 sheet: None (None), residues: 0 loop : -3.20 (0.45), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 122 HIS 0.005 0.001 HIS A 191 PHE 0.012 0.001 PHE A 370 TYR 0.017 0.001 TYR A 267 ARG 0.002 0.000 ARG A 356 Details of bonding type rmsd hydrogen bonds : bond 0.05662 ( 116) hydrogen bonds : angle 6.03539 ( 348) SS BOND : bond 0.00084 ( 1) SS BOND : angle 0.15686 ( 2) covalent geometry : bond 0.00322 ( 3572) covalent geometry : angle 0.56712 ( 4875) *********************** 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 68 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.478 Fit side-chains REVERT: A 76 MET cc_start: 0.7677 (tpp) cc_final: 0.7424 (tpp) REVERT: A 364 TRP cc_start: 0.8214 (t60) cc_final: 0.7908 (t60) outliers start: 10 outliers final: 9 residues processed: 67 average time/residue: 0.1252 time to fit residues: 10.8519 Evaluate side-chains 64 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.334 ------------------------------------------------------------------------------- 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 204 THR 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 14 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 35 optimal weight: 0.0870 chunk 1 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 overall best weight: 0.7558 ------------------------------------------------------------------------------- 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 = 0.3715 r_free = 0.3715 target = 0.153840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.133281 restraints weight = 4428.494| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.05 r_work: 0.3307 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3573 Z= 0.153 Angle : 0.552 5.989 4877 Z= 0.298 Chirality : 0.041 0.126 537 Planarity : 0.004 0.047 588 Dihedral : 5.888 50.989 464 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.93 % Allowed : 15.45 % Favored : 80.62 % 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: -3.98 (0.36), residues: 427 helix: -2.28 (0.27), residues: 298 sheet: None (None), residues: 0 loop : -3.11 (0.47), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 122 HIS 0.005 0.001 HIS A 191 PHE 0.011 0.001 PHE A 123 TYR 0.014 0.001 TYR A 267 ARG 0.002 0.001 ARG A 356 Details of bonding type rmsd hydrogen bonds : bond 0.05233 ( 116) hydrogen bonds : angle 5.78593 ( 348) SS BOND : bond 0.00081 ( 1) SS BOND : angle 0.10258 ( 2) covalent geometry : bond 0.00356 ( 3572) covalent geometry : angle 0.55194 ( 4875) *********************** 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 76 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.315 Fit side-chains REVERT: A 62 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.8286 (pt0) REVERT: A 107 ARG cc_start: 0.8812 (mtt180) cc_final: 0.8511 (mtt180) REVERT: A 195 ILE cc_start: 0.8957 (tp) cc_final: 0.8640 (tp) REVERT: A 261 LYS cc_start: 0.7166 (ttpt) cc_final: 0.6725 (tttp) REVERT: A 364 TRP cc_start: 0.8260 (t60) cc_final: 0.7946 (t60) outliers start: 14 outliers final: 11 residues processed: 72 average time/residue: 0.1350 time to fit residues: 12.2766 Evaluate side-chains 69 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.331 ------------------------------------------------------------------------------- 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 191 HIS Chi-restraints excluded: chain A residue 204 THR 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 22 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3655 r_free = 0.3655 target = 0.149735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.129189 restraints weight = 4496.987| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.03 r_work: 0.3385 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3573 Z= 0.147 Angle : 0.543 5.723 4877 Z= 0.292 Chirality : 0.041 0.120 537 Planarity : 0.004 0.045 588 Dihedral : 5.652 48.404 464 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.93 % Allowed : 16.57 % 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 (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: -3.66 (0.37), residues: 427 helix: -2.04 (0.28), residues: 298 sheet: None (None), residues: 0 loop : -3.00 (0.47), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 122 HIS 0.006 0.001 HIS A 191 PHE 0.010 0.001 PHE A 123 TYR 0.016 0.001 TYR A 267 ARG 0.002 0.001 ARG A 453 Details of bonding type rmsd hydrogen bonds : bond 0.05038 ( 116) hydrogen bonds : angle 5.63902 ( 348) SS BOND : bond 0.00098 ( 1) SS BOND : angle 0.03720 ( 2) covalent geometry : bond 0.00341 ( 3572) covalent geometry : angle 0.54268 ( 4875) *********************** 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 72 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.359 Fit side-chains REVERT: A 62 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.8168 (pt0) REVERT: A 105 ARG cc_start: 0.8201 (mmm-85) cc_final: 0.7677 (mmt90) REVERT: A 195 ILE cc_start: 0.8871 (tp) cc_final: 0.8543 (tp) REVERT: A 261 LYS cc_start: 0.7188 (ttpt) cc_final: 0.6719 (tttp) REVERT: A 364 TRP cc_start: 0.8260 (t60) cc_final: 0.7952 (t60) REVERT: A 418 MET cc_start: 0.6962 (mtp) cc_final: 0.6532 (mtp) outliers start: 14 outliers final: 11 residues processed: 71 average time/residue: 0.1480 time to fit residues: 13.1073 Evaluate side-chains 69 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.359 ------------------------------------------------------------------------------- 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 204 THR 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 436 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 0.3980 chunk 8 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 15 optimal weight: 0.3980 chunk 30 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3626 r_free = 0.3626 target = 0.147650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.127064 restraints weight = 4546.793| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.05 r_work: 0.3249 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3573 Z= 0.142 Angle : 0.538 5.592 4877 Z= 0.288 Chirality : 0.041 0.128 537 Planarity : 0.004 0.044 588 Dihedral : 5.499 47.528 464 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.93 % Allowed : 17.13 % 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 (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: -3.40 (0.37), residues: 427 helix: -1.82 (0.29), residues: 298 sheet: None (None), residues: 0 loop : -2.95 (0.48), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 122 HIS 0.002 0.001 HIS A 226 PHE 0.010 0.001 PHE A 123 TYR 0.013 0.001 TYR A 267 ARG 0.002 0.001 ARG A 453 Details of bonding type rmsd hydrogen bonds : bond 0.04863 ( 116) hydrogen bonds : angle 5.46932 ( 348) SS BOND : bond 0.00097 ( 1) SS BOND : angle 0.07833 ( 2) covalent geometry : bond 0.00335 ( 3572) covalent geometry : angle 0.53856 ( 4875) *********************** 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 76 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.355 Fit side-chains REVERT: A 62 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.8213 (pt0) REVERT: A 105 ARG cc_start: 0.8080 (mmm-85) cc_final: 0.7527 (mmt90) REVERT: A 111 GLU cc_start: 0.8814 (pt0) cc_final: 0.8561 (pt0) REVERT: A 134 TRP cc_start: 0.8650 (m100) cc_final: 0.8199 (m100) REVERT: A 195 ILE cc_start: 0.8871 (tp) cc_final: 0.8463 (tp) REVERT: A 364 TRP cc_start: 0.8251 (t60) cc_final: 0.8005 (t60) REVERT: A 418 MET cc_start: 0.7126 (mtp) cc_final: 0.6745 (mtp) outliers start: 14 outliers final: 13 residues processed: 74 average time/residue: 0.1502 time to fit residues: 13.9307 Evaluate side-chains 69 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 0.358 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 10 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3671 r_free = 0.3671 target = 0.150491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.129963 restraints weight = 4433.095| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.02 r_work: 0.3268 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3573 Z= 0.149 Angle : 0.544 5.655 4877 Z= 0.291 Chirality : 0.042 0.119 537 Planarity : 0.004 0.044 588 Dihedral : 5.445 47.398 464 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.93 % Allowed : 17.42 % 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 (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: -3.28 (0.38), residues: 427 helix: -1.73 (0.29), residues: 298 sheet: None (None), residues: 0 loop : -2.92 (0.48), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 122 HIS 0.002 0.001 HIS A 226 PHE 0.013 0.001 PHE A 417 TYR 0.014 0.001 TYR A 267 ARG 0.002 0.001 ARG A 453 Details of bonding type rmsd hydrogen bonds : bond 0.04814 ( 116) hydrogen bonds : angle 5.48131 ( 348) SS BOND : bond 0.00095 ( 1) SS BOND : angle 0.06005 ( 2) covalent geometry : bond 0.00351 ( 3572) covalent geometry : angle 0.54437 ( 4875) *********************** 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 72 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.426 Fit side-chains REVERT: A 62 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.8175 (pt0) REVERT: A 105 ARG cc_start: 0.8077 (mmm-85) cc_final: 0.7517 (mmt90) REVERT: A 134 TRP cc_start: 0.8634 (m100) cc_final: 0.8206 (m100) REVERT: A 195 ILE cc_start: 0.8890 (tp) cc_final: 0.8497 (tp) REVERT: A 225 LYS cc_start: 0.7006 (mtmp) cc_final: 0.6759 (mttm) REVERT: A 364 TRP cc_start: 0.8257 (t60) cc_final: 0.8008 (t60) REVERT: A 418 MET cc_start: 0.7162 (mtp) cc_final: 0.6767 (mtp) outliers start: 14 outliers final: 13 residues processed: 70 average time/residue: 0.1399 time to fit residues: 12.4298 Evaluate side-chains 71 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.335 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 12 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 0.0070 chunk 16 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 19 optimal weight: 0.5980 overall best weight: 0.6200 ------------------------------------------------------------------------------- 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 = 0.3629 r_free = 0.3629 target = 0.147559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.127063 restraints weight = 4411.865| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.00 r_work: 0.3241 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.3279 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 : 0.530 5.615 4877 Z= 0.283 Chirality : 0.041 0.116 537 Planarity : 0.004 0.043 588 Dihedral : 5.346 46.927 464 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.65 % Allowed : 17.98 % Favored : 78.37 % 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: -3.14 (0.38), residues: 427 helix: -1.61 (0.29), residues: 294 sheet: None (None), residues: 0 loop : -2.87 (0.47), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 122 HIS 0.002 0.001 HIS A 191 PHE 0.012 0.001 PHE A 417 TYR 0.014 0.001 TYR A 267 ARG 0.002 0.000 ARG A 356 Details of bonding type rmsd hydrogen bonds : bond 0.04635 ( 116) hydrogen bonds : angle 5.41538 ( 348) SS BOND : bond 0.00045 ( 1) SS BOND : angle 0.04395 ( 2) covalent geometry : bond 0.00312 ( 3572) covalent geometry : angle 0.53012 ( 4875) *********************** 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 71 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.342 Fit side-chains REVERT: A 62 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.8224 (pt0) REVERT: A 105 ARG cc_start: 0.8066 (mmm-85) cc_final: 0.7519 (mmt90) REVERT: A 134 TRP cc_start: 0.8543 (m100) cc_final: 0.8021 (m100) REVERT: A 195 ILE cc_start: 0.8875 (tp) cc_final: 0.8460 (tp) REVERT: A 364 TRP cc_start: 0.8181 (t60) cc_final: 0.7964 (t60) REVERT: A 418 MET cc_start: 0.7233 (mtp) cc_final: 0.6865 (mtp) REVERT: A 440 PHE cc_start: 0.8890 (t80) cc_final: 0.8443 (t80) outliers start: 13 outliers final: 12 residues processed: 69 average time/residue: 0.1306 time to fit residues: 11.5312 Evaluate side-chains 70 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.334 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 5 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 40 optimal weight: 0.0670 chunk 30 optimal weight: 0.0370 chunk 18 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- 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 = 0.3668 r_free = 0.3668 target = 0.150626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.130076 restraints weight = 4336.407| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.01 r_work: 0.3268 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3573 Z= 0.113 Angle : 0.524 6.020 4877 Z= 0.278 Chirality : 0.040 0.114 537 Planarity : 0.004 0.044 588 Dihedral : 5.225 46.263 464 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 4.21 % Allowed : 17.13 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.38), residues: 427 helix: -1.46 (0.29), residues: 300 sheet: None (None), residues: 0 loop : -2.85 (0.49), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 122 HIS 0.008 0.001 HIS A 191 PHE 0.011 0.001 PHE A 417 TYR 0.013 0.001 TYR A 267 ARG 0.002 0.000 ARG A 194 Details of bonding type rmsd hydrogen bonds : bond 0.04397 ( 116) hydrogen bonds : angle 5.30999 ( 348) SS BOND : bond 0.00077 ( 1) SS BOND : angle 0.12508 ( 2) covalent geometry : bond 0.00258 ( 3572) covalent geometry : angle 0.52446 ( 4875) *********************** 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 75 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.390 Fit side-chains REVERT: A 62 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.8211 (pt0) REVERT: A 134 TRP cc_start: 0.8516 (m100) cc_final: 0.8018 (m100) REVERT: A 195 ILE cc_start: 0.8875 (tp) cc_final: 0.8454 (tp) REVERT: A 364 TRP cc_start: 0.8163 (t60) cc_final: 0.7948 (t60) REVERT: A 418 MET cc_start: 0.7271 (mtp) cc_final: 0.6923 (mtp) REVERT: A 440 PHE cc_start: 0.8870 (t80) cc_final: 0.8435 (t80) outliers start: 15 outliers final: 14 residues processed: 72 average time/residue: 0.1282 time to fit residues: 12.0379 Evaluate side-chains 70 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 0.334 ------------------------------------------------------------------------------- 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 323 PHE Chi-restraints excluded: chain A residue 339 LYS Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 370 PHE 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 36 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 12 optimal weight: 0.2980 chunk 20 optimal weight: 0.9990 chunk 21 optimal weight: 0.0570 chunk 26 optimal weight: 0.0020 chunk 24 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 overall best weight: 0.3906 ------------------------------------------------------------------------------- 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 = 0.3694 r_free = 0.3694 target = 0.152589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.132143 restraints weight = 4397.003| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.02 r_work: 0.3278 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.3470 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= 0.109 Angle : 0.512 5.371 4877 Z= 0.273 Chirality : 0.040 0.111 537 Planarity : 0.004 0.044 588 Dihedral : 5.109 45.528 464 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 4.21 % Allowed : 17.13 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.39), residues: 427 helix: -1.29 (0.30), residues: 298 sheet: None (None), residues: 0 loop : -2.72 (0.49), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 122 HIS 0.003 0.001 HIS A 191 PHE 0.011 0.001 PHE A 417 TYR 0.015 0.001 TYR A 267 ARG 0.003 0.000 ARG A 194 Details of bonding type rmsd hydrogen bonds : bond 0.04226 ( 116) hydrogen bonds : angle 5.25996 ( 348) SS BOND : bond 0.00093 ( 1) SS BOND : angle 0.14156 ( 2) covalent geometry : bond 0.00248 ( 3572) covalent geometry : angle 0.51201 ( 4875) ********************** 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 73 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.380 Fit side-chains REVERT: A 62 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.8199 (pt0) REVERT: A 134 TRP cc_start: 0.8543 (m100) cc_final: 0.8035 (m100) REVERT: A 195 ILE cc_start: 0.8851 (tp) cc_final: 0.8496 (tp) REVERT: A 225 LYS cc_start: 0.6931 (mtmp) cc_final: 0.6657 (mttm) REVERT: A 364 TRP cc_start: 0.8191 (t60) cc_final: 0.7949 (t60) REVERT: A 418 MET cc_start: 0.7336 (mtp) cc_final: 0.7006 (mtp) REVERT: A 440 PHE cc_start: 0.8850 (t80) cc_final: 0.8426 (t80) outliers start: 15 outliers final: 12 residues processed: 69 average time/residue: 0.1407 time to fit residues: 12.4573 Evaluate side-chains 70 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.369 ------------------------------------------------------------------------------- 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 323 PHE 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 5 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 21 optimal weight: 0.1980 chunk 0 optimal weight: 7.9990 chunk 6 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 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 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 = 0.3713 r_free = 0.3713 target = 0.153754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.133532 restraints weight = 4420.397| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.99 r_work: 0.3264 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.3499 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 : 0.528 5.447 4877 Z= 0.280 Chirality : 0.041 0.116 537 Planarity : 0.004 0.042 588 Dihedral : 5.119 45.448 464 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.93 % Allowed : 17.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.39), residues: 427 helix: -1.23 (0.29), residues: 299 sheet: None (None), residues: 0 loop : -2.68 (0.50), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 122 HIS 0.008 0.001 HIS A 191 PHE 0.012 0.001 PHE A 417 TYR 0.014 0.001 TYR A 267 ARG 0.002 0.001 ARG A 194 Details of bonding type rmsd hydrogen bonds : bond 0.04409 ( 116) hydrogen bonds : angle 5.27226 ( 348) SS BOND : bond 0.00099 ( 1) SS BOND : angle 0.04661 ( 2) covalent geometry : bond 0.00315 ( 3572) covalent geometry : angle 0.52815 ( 4875) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2181.77 seconds wall clock time: 38 minutes 11.01 seconds (2291.01 seconds total)